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Contact Molecules for Homologous Proteins


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PID QueryLength Homolgous Sequence in PDB UniProt Query TITLE
2691701 207 1500 P51149(RAB7A_HUMAN) RecName: Full=Ras-related protein Rab-7a ; EC=3.6.5.2 ;
QUERYSEQ
MTSRKKVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIP
YFETSAKEAINVEQAFQTIARNALKQETEVELYNEFPEPIKLDKNDRAKASAESCSC
[BLAST file for PDB] (plain) (bar) (multiple alignment) [BLAST for UniProt: (plain) (bar) (multiple alignment) (PSSM file) ]

Statistics of sites in view of Disease classification

All 600882 Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) LB/B (likely benign or benign)
Number of sites 207 4 1
Buired or ExposedBuried 41.1 (%) [79] 25.0 (%) [1] 0.0 (%) [0]
Exposed 58.9 (%) [113] 75.0 (%) [3] 100.0 (%) [1]
Ave relacc 32.9 % 30.8 % 56.1 %
SD relacc 29.15 % 16.91 % 0.00 %
Contact Molhetero 79.7 (%) [165] 100.0 (%) [4] 100.0 (%) [1]
nucleotide 4.3 (%) [9] 0.0 (%) [0] 0.0 (%) [0]
compound 54.1 (%) [112] 75.0 (%) [3] 100.0 (%) [1]
metal 58.0 (%) [120] 100.0 (%) [4] 100.0 (%) [1]
otherpoly 0.0 (%) [0] 0.0 (%) [0] 0.0 (%) [0]
homo 73.4 (%) [152] 100.0 (%) [4] 100.0 (%) [1]
precipitant 72.9 (%) [151] 100.0 (%) [4] 100.0 (%) [1]
Number of variants 5 4 1
N_Freq(AAvariant)==0 % 25.0 % [1] 0.0 % [0]
N_Freq(AAvariant)>0 % 75.0 % [3] 100.0 % [1]
Ave Freq(AAvariant) 1.0 % 17.0 %
SD Freq(AAvariant) 0.71 % 0.00 %

Site Table for OMIM:600882 Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) [4 variants]

4 sites 129,157,161,162
  [n]:site number of query sequence.  [a]:amino acid of query sequence.  [s]:predicted secondary structure.
  [e]:predicted exposed/buried.  [acc]:predicted relative accesssibility(%).  [pdb]:PDB code of homologous structure.
  [contact_mols]:predicted binding molecules  [observed aa]:Observed amino acids among homologous sequences.  [feature table]:UniProt Feature Table
  [variant]:UniProt Human Variant.
n a s e acc pdb contact_mols observed aa feature table variant
129LSe 44.4 1vg8_D hetero PI4KB_HUMAN RAB3I_HUMAN VIRA_SHIFL TNPO1_HUMAN XPO1_YEAST KA122_YEAST CSE1_YEAST O52121_ECOLX Q5WMC0_ECOLX PI4KB_BOVIN compound GDP GNP GTP GSP GCP CAG 6ZD BTB DBG G3D Y9Z VJ8 VJB metal UNX homo precipitant
LMIVKARCDEFHPQST
L->F:(1.0 %):LP/P Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) dbSNP:rs1219090 [MIM:600882]
157KTe 41.0 1vg8_D hetero PI4KB_HUMAN RAB3I_HUMAN RPGF4_MOUSE SOS1_HUMAN IMB1_YEAST RASK_HUMAN A2ASW3_MOUSE XPOT_SCHPO SHOC2_HUMAN IMB5_YEAST CSE1_YEAST XPO1_MOUSE IF5A1_HUMAN PI4KB_BOVIN KA122_YEAST ANKX_LEGPH IPO9_HUMAN compound GDP GNP GTP GCP GSP CAG 2UK 6ZD AGN GNH DBG G3D RSG Y9Z 2UH 2UJ VJ8 VJB metal CL K homo precipitant
KLARTMSEFIQV
BINDING /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565" ECO:0000269|PubMed:20028791" BINDING /ligand="GTP" /ligand_id="ChEBI:CHEBI:37565" ECO:0000269|PubMed:20028791" K->N:(0.0 %):LP/P Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) dbSNP:rs1219090 [MIM:600882]
161NSe 35.8 1vg8_D hetero XPO1_YEAST RBP2_HUMAN TR120_YEAST IMB1_YEAST TNPO1_HUMAN XPOT_SCHPO IMB1_HUMAN TNPO3_HUMAN W7PTE1_YEASX ANKX_LEGPH IMB5_YEAST compound 17F GLC metal UNX CL homo precipitant
NGSHRTCDEKLQ
N->T:(2.0 %):LP/P Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) dbSNP:rs1219090 [MIM:600882]
162VHb 2.0 1vg8_D hetero YRB1_YEAST RBP2_HUMAN A0A6A5PZB5_YEASX IMB1_YEAST TNPO1_HUMAN NUP50_HUMAN RANG_HUMAN YRB2_YEAST metal CL UNX homo precipitant
VILFTAEKMY
V->M:(1.0 %):LP/P Charcot-Marie-Tooth disease, axonal, 2B (CMT2B) dbSNP:rs1219090 [MIM:600882]

Site Table for OMIM:LB/B [1 variants]

1 sites 32
  [n]:site number of query sequence.  [a]:amino acid of query sequence.  [s]:predicted secondary structure.
  [e]:predicted exposed/buried.  [acc]:predicted relative accesssibility(%).  [pdb]:PDB code of homologous structure.
  [contact_mols]:predicted binding molecules  [observed aa]:Observed amino acids among homologous sequences.  [feature table]:UniProt Feature Table
  [variant]:UniProt Human Variant.
n a s e acc pdb contact_mols observed aa feature table variant
32K e 56.1 1vg8_D hetero YRB1_YEAST SOS1_HUMAN RBP2_HUMAN A0A6A5PZB5_YEASX KRIT1_HUMAN RANG_HUMAN 3BP5_HUMAN PP1A_HUMAN SEC2_YEAST RPGF4_MOUSE RASK_HUMAN RBP1_HUMAN IMB1_YEAST MYO5B_HUMAN RAF1_HUMAN SEC5_RAT Q9HBX6_HUMAN RASF5_MOUSE YRB2_YEAST PI4KB_HUMAN MYO5A_HUMAN G0SGS3_CHATD DRRA_LEGPN SIN1_HUMAN NUP50_HUMAN RGL2_HUMAN AB1IP_MOUSE TNPO3_HUMAN IF5A1_HUMAN PI4KB_BOVIN TLN1_MOUSE SHAN3_MOUSE ANKX_LEGPH PP1G_HUMAN IPO9_HUMAN compound GDP metal UNX MG NA ZN CO homo precipitant
ERKQTSAHDIGNPVCLMY
K->E:(17.0 %):LB/B - dbSNP:rs1154975