Research workbench
RAB6-GTP:GCC185 rab binding domain complex
Analyse RAB6-GTP:GCC185 rab binding domain complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BBP
- Type
- protein
- Length
- 588 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-6A; Grip and coiled-coil domain-containing protein 2
- UniProt
- P20340, Q8IWJ2
- Ligands
- GTP, MG
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | RAS-related protein rab-6A | protein | 161 | 35% helix, 29% strand | P20340 |
| D | Grip and coiled-coil domain-containing protein 2 | protein | 38 | 84% helix, 0% strand | Q8IWJ2 |
| E | Grip and coiled-coil domain-containing protein 2 | protein | 37 | 86% helix, 0% strand | Q8IWJ2 |
| F | Grip and coiled-coil domain-containing protein 2 | protein | 30 | 90% helix, 0% strand | Q8IWJ2 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.59 | 0.77 | 51 | GTP |
| 2 | 276 | 0.58 | 0.78 | 48 | GTP |
| 3 | 271 | 0.58 | 0.78 | 46 | GTP |
| 4 | 89 | 0.35 | 0.74 | 13 | empty |
| 5 | 81 | 0.35 | 0.74 | 13 | empty |
Interfaces
6 interfaces between chains.
- D–E · 967 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 440 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 422 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 307 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 302 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3BBP · Rab6-GTP:GCC185 Rab binding domain complex · the same entry in another collection · chain F against F, TM-score 1.00
- P20340 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-6A (P20340) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q8IWJ2 · AlphaFold monomer V2.0 prediction for grip and coiled-coil domain- containing protein 2… · a predicted model of the same protein · chain F against A, TM-score 0.87
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 P20340
- Every structure of UniProt Q8IWJ2
- Elsewhere: RCSB PDB 3BBP · PDBe 3BBP · UniProt P20340 · UniProt Q8IWJ2
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