MolNFT v1 · #25123 · protein
The crystal structures of the rep-1 protein in complex with C- terminally truncated RAB7 protein
1VG9 · Rab proteins geranylgeranyltransferase component a 1: “The crystal structures of the rep-1 protein in complex with C- terminally truncated RAB7 protein”. X-ray diffraction, 3 ligands (GDP, MG, K), 20 pockets (best druggability…
- PDB
- 1VG9
- Type
- protein
- Length
- 2,688 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rab proteins geranylgeranyltransferase component a 1; RAS-related protein rab-7
- UniProt
- P37727, P09527
- Ligands
- GDP, MG, K
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rab proteins geranylgeranyltransferase component a 1 | protein | 501 | 31% helix, 25% strand | P37727 |
| B | RAS-related protein rab-7 | protein | 169 | 36% helix, 24% strand | P09527 |
| C, G | Rab proteins geranylgeranyltransferase component a 1 | protein | 502 | 30% helix, 24% strand | P37727 |
| D, H | RAS-related protein rab-7 | protein | 173 | 39% helix, 24% strand | P09527 |
| E | Rab proteins geranylgeranyltransferase component a 1 | protein | 500 | 31% helix, 25% strand | P37727 |
| F | RAS-related protein rab-7 | protein | 168 | 35% helix, 24% strand | P09527 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains B, D, F, H
- MG · Magnesium ion · metal · 4 copies · chains B, D, F, H
- K · Potassium ion · metal · 4 copies · chains B, D, F, H
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.81 | 0.82 | 130 | MG, GDP |
| 2 | 1046 | 0.80 | 0.81 | 122 | MG |
| 3 | 529 | 0.75 | 0.83 | 61 | empty |
| 4 | 440 | 0.75 | 0.84 | 62 | empty |
| 5 | 587 | 0.73 | 0.80 | 64 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1137 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 1136 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 1052 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1051 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1046 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1VG9 · The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7… · the same entry in another collection · chain H against H, TM-score 1.00
- P37727 · AlphaFold monomer V2.0 prediction for rab proteins geranylgeranyltransferase component a… · a predicted model of the same protein · chain C against A, TM-score 0.99
- P09527 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-7A (P09527) · a predicted model of the same protein · chain F against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P37727
- Every structure of UniProt P09527
- Elsewhere: RCSB PDB 1VG9 · PDBe 1VG9 · UniProt P37727 · UniProt P09527
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