Research workbench
The crystal structures of the rep-1 protein in complex with monoprenylated RAB7 protein
Analyse The crystal structures of the rep-1 protein in complex with monoprenylated RAB7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VG0
- Type
- protein
- Length
- 663 residues
- Chains
- 2
- 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
- GER, GDP, MG, CL
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rab proteins geranylgeranyltransferase component a 1 | protein | 481 | 33% helix, 24% strand | P37727 |
| B | RAS-related protein rab-7 | protein | 182 | 36% helix, 24% strand | P09527 |
Ligands and binding sites
- GER · Geran-8-yl geran · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.81 | 0.82 | 88 | PG4 |
| 2 | 464 | 0.70 | 0.80 | 49 | CL |
| 3 | 197 | 0.63 | 0.83 | 30 | GER |
| 4 | 71 | 0.45 | 0.82 | 18 | empty |
| 5 | 102 | 0.43 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1523 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1VG0 · The crystal structures of the REP-1 protein in complex with monoprenylated Rab7 protein · the same entry in another collection · chain A against A, TM-score 1.00
- P37727 · AlphaFold monomer V2.0 prediction for rab proteins geranylgeranyltransferase component a… · a predicted model of the same protein · chain A against A, TM-score 1.00
- P09527 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-7A (P09527) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 1VG0 · PDBe 1VG0 · UniProt P37727 · UniProt P09527
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