Contact Molecules for Homologous Proteins

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PID QueryLength Homolgous Sequence in PDB UniProt Query TITLE
2624989 215 52 P09429(HMGB1_HUMAN) RecName: Full=High mobility group protein B1;AltName: Full=High mobility group protein 1; Short=HMG-1;
QUERYSEQ 
MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK
LKEKYEKDIAAYRAKGKPDAAKKGVVKAEKSKKKKEEEEDEEDEEDEEEEEDEEDEDEEEDDDDE
[BLAST file for PDB] (plain) (bar) (multiple alignment) [BLAST for UniProt: (plain) (bar) (multiple alignment) (PSSM file) ]

UniProt Feature Tables [P09429(HMGB1_HUMAN)]

215
region name description
1-215 CHAIN /note="High mobility group protein B1" /id="PRO_0000048526"
9-79 DNA_BIND /note="HMG box 1"
95-163 DNA_BIND /note="HMG box 2"
1-97 REGION /note="Sufficient for interaction with HAVCR2"
3-15 REGION /note="LPS binding (delipidated)"
76-95 REGION /note="Disordered"
80-96 REGION /note="LPS binding (Lipid A)"
89-108 REGION /note="Cytokine-stimulating activity"
150-183 REGION /note="Binding to AGER/RAGE"
161-215 REGION /note="Disordered"
76-94 COMPBIAS /note="Basic and acidic residues"
161-187 COMPBIAS /note="Basic and acidic residues"
188-215 COMPBIAS /note="Acidic residues"
1-10 BINDING /ligand="heparin" /ligand_id="ChEBI:CHEBI:28304"
1-215 DISORDER predicted by DISOPRED

MONOMER
215
pdb_id a1 identity[%]2 description
2yrq A 100.0 HMGB1_HUMAN High mobility group protein B1
6cij G 100.0 HMGB1_HUMAN High mobility group protein B1
5ze0 E 100.0 HMGB1_MOUSE HMGB1 A-B box
5ze1 E 100.0 HMGB1_MOUSE HMGB1 A-B box
5zdz E 100.0 HMGB1_MOUSE HMGB1 A-B box
5ze2 E 100.0 HMGB1_MOUSE HMGB1 A-B box
2rtu A 100.0 HMGB1_HUMAN High mobility group protein B1
2ly4 A 100.0 HMGB1_HUMAN High mobility group protein B1
2gzk C 67.1 Q6J415_HUMAN Q548R9_RAT Sex-determining region on Y / HMGB1
1aab A 98.8 HMG1_RAT HIGH MOBILITY GROUP PROTEIN
1hsn A 100.0 HMG1_CRIGR HIGH MOBILITY GROUP PROTEIN 1
1hsm A 100.0 HMG1_CRIGR HIGH MOBILITY GROUP PROTEIN 1
1nhn A 100.0 HMG1_CRIGR HIGH MOBILITY GROUP PROTEIN 1
1nhm A 100.0 HMG1_CRIGR HIGH MOBILITY GROUP PROTEIN 1
1hmf A 100.0 HMG1_RAT HIGH MOBILITY GROUP PROTEIN FRAGMENT-B
1hme A 100.0 HMG1_RAT HIGH MOBILITY GROUP PROTEIN FRAGMENT-B
8i9m A 100.0 HMGB1_HUMAN High mobility group protein B1
4qr9 A 100.0 HMGB1_RAT High mobility group protein B1
4qr9 B 100.0 HMGB1_RAT High mobility group protein B1
6cik E 100.0 HMGB1_HUMAN High mobility group protein B1
6cim E 100.0 HMGB1_HUMAN High mobility group protein B1
1ckt C 100.0 HMG1_RAT HIGH MOBILITY GROUP 1 PROTEIN
1j3x A 89.6 HMG2_PIG High mobility group protein 2
6cg0 K 100.0 HMGB1_HUMAN High mobility group protein B1
1j3c A 89.5 HMG2_PIG High mobility group protein 2
1j3d A 88.2 HMG2_PIG High mobility group protein 2
2yqi A 77.0 HMGB3_HUMAN High mobility group protein B3
6oem J 100.0 HMGB1_HUMAN High mobility group protein B1
6oen J 100.0 HMGB1_HUMAN High mobility group protein B1
2eqz A 80.3 HMGB3_HUMAN High mobility group protein B3
6oeo I 100.0 HMGB1_HUMAN High mobility group protein B1
6cil E 100.0 HMGB1_HUMAN High mobility group protein B1
6oem I 100.0 HMGB1_HUMAN High mobility group protein B1
6oen I 100.0 HMGB1_HUMAN High mobility group protein B1
6oer I 100.0 HMGB1_HORSE High mobility group protein B1
1cg7 A 45.9 NHP6A_YEAST PROTEIN (NON HISTONE PROTEIN 6 A)
1lwm A 45.9 NHP6A_YEAST NONHISTONE CHROMOSOMAL PROTEIN 6A
1j5n C 45.9 NHP6A_YEAST Nonhistone chromosomal protein 6A
6l34 A 41.8 SSRP1_HUMAN FACT complex subunit SSRP1
1qrv C 44.3 HMGD_DROME HIGH MOBILITY GROUP PROTEIN D
1hma A 44.3 HMGD_DROME HMG-D
1e7j A 44.3 HMGD_DROME HIGH MOBILITY GROUP PROTEIN D
2co9 A 41.9 Q8R4H0_MOUSE thymus high mobility group box protein TOX
3nm9 F 44.3 HMGD_DROME High mobility group protein D
3nm9 E 44.3 HMGD_DROME High mobility group protein D
3nm9 D 44.3 HMGD_DROME High mobility group protein D
3nm9 A 44.3 HMGD_DROME High mobility group protein D
3nm9 C 44.3 HMGD_DROME High mobility group protein D
3nm9 B 44.3 HMGD_DROME High mobility group protein D
1qrv D 46.0 HMGD_DROME HIGH MOBILITY GROUP PROTEIN D
2mrc A 42.3 Q8IB14_PLAF7 High mobility group protein
1wxl A 40.6 SSRP_DROME Single-strand recognition protein 
1.a1:asym_id for the homologue. 2.identity[%]2:sequence identity between the query and the homologue.
HETERO
215 pdb_id contact mol homologue
a3 description a4 identity[%]5 Ncon6 description
2ly4 B P53_HUMAN Cellular tumor antigen p53[47 aa] A 100.0
/100.0		 17
/17		 HMGB1_HUMAN High mobility group protein B1
6cij A RAG1_MOUSE V(D)J recombination-activating protein 1[614 aa] G 100.0
/100.0		 3
/3		 HMGB1_HUMAN High mobility group protein B1
6cij B RAG1_MOUSE V(D)J recombination-activating protein 1[616 aa] G 100.0
/100.0		 1
/1		 HMGB1_HUMAN High mobility group protein B1
8i9m B RAGE_HUMAN Advanced glycosylation end product-specific recept.. A 100.0
/100.0		 14
/14		 HMGB1_HUMAN High mobility group protein B1
3.a3:asym_id for the contact molecule. 4.a4:asym_id for the template homologue. 5.identity[%]5:sequence identity between the query and the template homologue only for the contact residues. Number after the slash / is sequence identity for all the aligned region. 6.Ncon6:number of aligned contact residues for the query. Number after the slash / is number of contact residues in the template homologue.
NUCLEOTIDE
215 pdb_id contact mol homologue
a3 description a4 identity[%]5 Ncon6 description
1ckt A DNA (5'-D(*CP*CP*(5IU)P*CP*TP*CP*TP*GP*GP*AP*CP*CP.. C 100.0
/100.0		 9
/9		 HMG1_RAT HIGH MOBILITY GROUP 1 PROTEIN
1ckt B DNA (5'-D(*GP*GP*AP*AP*GP*GP*TP*CP*CP*AP*GP*AP*GP*.. C 100.0
/100.0		 10
/10		 HMG1_RAT HIGH MOBILITY GROUP 1 PROTEIN
4qr9 C DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3') A 100.0
/100.0		 11
/11		 HMGB1_RAT High mobility group protein B1
4qr9 D DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3') A 100.0
/100.0		 10
/11		 HMGB1_RAT High mobility group protein B1
4qr9 F DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3') A 100.0
/100.0		 2
/4		 HMGB1_RAT High mobility group protein B1
4qr9 C DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3') B 100.0
/100.0		 10
/11		 HMGB1_RAT High mobility group protein B1
4qr9 D DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3') B 100.0
/100.0		 11
/11		 HMGB1_RAT High mobility group protein B1
5zdz I DNA (39-MER) E 100.0
/100.0		 10
/10		 HMGB1_MOUSE HMGB1 A-B box
5ze0 I DNA (54-MER) E 100.0
/100.0		 12
/12		 HMGB1_MOUSE HMGB1 A-B box
5ze1 I DNA E 100.0
/100.0		 10
/10		 HMGB1_MOUSE HMGB1 A-B box
5zdz K DNA chain M E 100.0
/100.0		 11
/11		 HMGB1_MOUSE HMGB1 A-B box
5ze0 K DNA (39-MER) E 100.0
/100.0		 11
/11		 HMGB1_MOUSE HMGB1 A-B box
5ze1 K DNA E 100.0
/100.0		 12
/12		 HMGB1_MOUSE HMGB1 A-B box
5ze2 H DNA (40-MER) E 100.0
/100.0		 7
/7		 HMGB1_MOUSE HMGB1 A-B box
5ze2 J DNA (40-MER) E 100.0
/100.0		 10
/10		 HMGB1_MOUSE HMGB1 A-B box
6cg0 H DNA (60-MER) K 100.0
/100.0		 12
/12		 HMGB1_HUMAN High mobility group protein B1
6cg0 J DNA (41-MER) K 100.0
/100.0		 11
/11		 HMGB1_HUMAN High mobility group protein B1
6cij K DNA (41-MER) G 100.0
/100.0		 12
/12		 HMGB1_HUMAN High mobility group protein B1
6cij F DNA (60-MER) G 100.0
/100.0		 10
/10		 HMGB1_HUMAN High mobility group protein B1
6cik H Nicked 23RSS intermediate reverse strand E 100.0
/100.0		 10
/10		 HMGB1_HUMAN High mobility group protein B1
6cik J Nicked 23RSS intermediate forward strand E 100.0
/100.0		 6
/6		 HMGB1_HUMAN High mobility group protein B1
6cil H Intact 23RSS substrate reverse strand E 100.0
/100.0		 5
/5		 HMGB1_HUMAN High mobility group protein B1
6cim I Intact 23RSS substrate reverse strand E 100.0
/100.0		 10
/10		 HMGB1_HUMAN High mobility group protein B1
6cim J Intact 23RSS substrate forward strand E 100.0
/100.0		 5
/5		 HMGB1_HUMAN High mobility group protein B1
6oem E DNA (57-MER) I 100.0
/100.0		 7
/7		 HMGB1_HUMAN High mobility group protein B1
6oen E DNA (57-MER) I 100.0
/100.0		 7
/7		 HMGB1_HUMAN High mobility group protein B1
6oem H DNA (57-MER) I 100.0
/100.0		 7
/7		 HMGB1_HUMAN High mobility group protein B1
6oen H DNA (57-MER) I 100.0
/100.0		 8
/8		 HMGB1_HUMAN High mobility group protein B1
6oer H DNA (57-MER) I 100.0
/100.0		 4
/4		 HMGB1_HORSE High mobility group protein B1
6oem F DNA (46-MER) J 100.0
/100.0		 8
/8		 HMGB1_HUMAN High mobility group protein B1
6oen F DNA (46-MER) J 100.0
/100.0		 8
/8		 HMGB1_HUMAN High mobility group protein B1
6oeo F DNA (46-MER) I 100.0
/100.0		 8
/8		 HMGB1_HUMAN High mobility group protein B1
6oem G DNA (46-MER) J 100.0
/100.0		 5
/5		 HMGB1_HUMAN High mobility group protein B1
6oen G DNA (46-MER) J 100.0
/100.0		 3
/3		 HMGB1_HUMAN High mobility group protein B1
6oeo E DNA (46-MER) I 100.0
/100.0		 2
/2		 HMGB1_HUMAN High mobility group protein B1
6oer G DNA (57-MER) I 100.0
/100.0		 5
/5		 HMGB1_HORSE High mobility group protein B1
2gzk A 5'-D(*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*GP.. C 71.4
/67.1		 28
/33		 Q6J415_HUMAN Q548R9_RAT Sex-determining region on Y / HMGB1
2gzk B 5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP.. C 75.0
/67.1		 24
/26		 Q6J415_HUMAN Q548R9_RAT Sex-determining region on Y / HMGB1
1qrv A DNA (5'-D(*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3') C 46.7
/44.3		 15
/16		 HMGD_DROME HIGH MOBILITY GROUP PROTEIN D
1qrv B DNA (5'-D(*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3') C 50.0
/44.3		 8
/8		 HMGD_DROME HIGH MOBILITY GROUP PROTEIN D
1qrv A DNA (5'-D(*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3') D 0.0
/46.0		 3
/3		 HMGD_DROME HIGH MOBILITY GROUP PROTEIN D
1qrv B DNA (5'-D(*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3') D 0.0
/46.0		 1
/1		 HMGD_DROME HIGH MOBILITY GROUP PROTEIN D
1j5n A 5'-D(*GP*GP*GP*GP*TP*GP*AP*TP*TP*GP*TP*TP*CP*AP*G).. C 33.3
/45.9		 12
/18		 NHP6A_YEAST Nonhistone chromosomal protein 6A
1j5n B 5'-D(*CP*TP*GP*AP*AP*CP*AP*AP*TP*CP*AP*CP*CP*CP*C).. C 61.5
/45.9		 13
/16		 NHP6A_YEAST Nonhistone chromosomal protein 6A
1e7j B DNA (5'-D(*CP*GP*AP*TP*AP*TP*TP*AP*AP*GP*AP*GP*CP*.. A 33.3
/44.3		 6
/6		 HMGD_DROME HIGH MOBILITY GROUP PROTEIN D
1e7j C DNA (5'-D(*GP*GP*CP*TP*CP*AP*AP*TP*AP*TP*CP*G)-3').. A 80.0
/44.3		 5
/5		 HMGD_DROME HIGH MOBILITY GROUP PROTEIN D
3nm9 G DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' A 50.0
/44.3		 2
/2		 HMGD_DROME High mobility group protein D
3nm9 H DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' A 66.7
/44.3		 3
/3		 HMGD_DROME High mobility group protein D
3nm9 O DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' A 60.0
/44.3		 5
/5		 HMGD_DROME High mobility group protein D
3nm9 P DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' A 66.7
/44.3		 6
/6		 HMGD_DROME High mobility group protein D
3nm9 I DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' B 57.1
/44.3		 7
/7		 HMGD_DROME High mobility group protein D
3nm9 J DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' B 60.0
/44.3		 5
/5		 HMGD_DROME High mobility group protein D
3nm9 P DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' B 0.0
/44.3		 1
/1		 HMGD_DROME High mobility group protein D
3nm9 I DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' C 100.0
/44.3		 4
/4		 HMGD_DROME High mobility group protein D
3nm9 J DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' C 60.0
/44.3		 5
/5		 HMGD_DROME High mobility group protein D
3nm9 K DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' C 50.0
/44.3		 4
/4		 HMGD_DROME High mobility group protein D
3nm9 L DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' C 50.0
/44.3		 4
/4		 HMGD_DROME High mobility group protein D
3nm9 J DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' D 100.0
/44.3		 1
/1		 HMGD_DROME High mobility group protein D
3nm9 M DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' D 40.0
/44.3		 5
/5		 HMGD_DROME High mobility group protein D
3nm9 O DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' E 75.0
/44.3		 8
/8		 HMGD_DROME High mobility group protein D
3nm9 P DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' E 60.0
/44.3		 5
/5		 HMGD_DROME High mobility group protein D
3nm9 M DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' F 71.4
/44.3		 7
/7		 HMGD_DROME High mobility group protein D
3nm9 N DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' B 100.0
/44.3		 4
/4		 HMGD_DROME High mobility group protein D
3nm9 N DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' D 40.0
/44.3		 5
/5		 HMGD_DROME High mobility group protein D
3nm9 N DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3' F 50.0
/44.3		 6
/6		 HMGD_DROME High mobility group protein D
3.a3:asym_id for the contact molecule. 4.a4:asym_id for the template homologue. 5.identity[%]5:sequence identity between the query and the template homologue only for the contact residues. Number after the slash / is sequence identity for all the aligned region. 6.Ncon6:number of aligned contact residues for the query. Number after the slash / is number of contact residues in the template homologue.
METAL
215 pdb_id contact mol homologue
a3 description a4 identity[%]5 Ncon6 description
1qrv E NA
SODIUM ION[1 atoms] 		C 0.0
/44.3		 1
/1		 HMGD_DROME HIGH MOBILITY GROUP PROTEIN D
3.a3:asym_id for the contact molecule. 4.a4:asym_id for the template homologue. 5.identity[%]5:sequence identity between the query and the template homologue only for the contact residues. Number after the slash / is sequence identity for all the aligned region. 6.Ncon6:number of aligned contact residues for the query. Number after the slash / is number of contact residues in the template homologue.
HOMO
215 pdb_id contact mol homologue
a3 description a4 identity[%]5 Ncon6 description
4qr9 B HMGB1_RAT High mobility group protein B1[75 aa] A 100.0
/100.0		 5
/5		 HMGB1_RAT High mobility group protein B1
4qr9 A HMGB1_RAT High mobility group protein B1[75 aa] B 100.0
/100.0		 5
/5		 HMGB1_RAT High mobility group protein B1
3nm9 E HMGD_DROME High mobility group protein D[73 aa] B 75.0
/44.3		 4
/4		 HMGD_DROME High mobility group protein D
3nm9 F HMGD_DROME High mobility group protein D[73 aa] B 66.7
/44.3		 6
/6		 HMGD_DROME High mobility group protein D
3nm9 D HMGD_DROME High mobility group protein D[73 aa] C 50.0
/44.3		 6
/6		 HMGD_DROME High mobility group protein D
3nm9 C HMGD_DROME High mobility group protein D[73 aa] D 57.1
/44.3		 7
/7		 HMGD_DROME High mobility group protein D
3nm9 B HMGD_DROME High mobility group protein D[73 aa] E 75.0
/44.3		 8
/8		 HMGD_DROME High mobility group protein D
3nm9 B HMGD_DROME High mobility group protein D[73 aa] F 57.1
/44.3		 7
/7		 HMGD_DROME High mobility group protein D
3.a3:asym_id for the contact molecule. 4.a4:asym_id for the template homologue. 5.identity[%]5:sequence identity between the query and the template homologue only for the contact residues. Number after the slash / is sequence identity for all the aligned region. 6.Ncon6:number of aligned contact residues for the query. Number after the slash / is number of contact residues in the template homologue.
PRECIPITANT
215 pdb_id contact mol homologue
a3 description a4 identity[%]5 Ncon6 description
1hsm B BME
BETA-MERCAPTOETHANOL[4 atoms] 		A 100.0
/100.0		 4
/4		 HMG1_CRIGR HIGH MOBILITY GROUP PROTEIN 1
1hsn B BME
BETA-MERCAPTOETHANOL[4 atoms] 		A 100.0
/100.0		 4
/4		 HMG1_CRIGR HIGH MOBILITY GROUP PROTEIN 1
3.a3:asym_id for the contact molecule. 4.a4:asym_id for the template homologue. 5.identity[%]5:sequence identity between the query and the template homologue only for the contact residues. Number after the slash / is sequence identity for all the aligned region. 6.Ncon6:number of aligned contact residues for the query. Number after the slash / is number of contact residues in the template homologue.