MolNFT v1 · #60616 · protein
Structure of RAB6(GTP)-R6IP1 complex
3CWZ · RAS-related protein rab-6A: “Structure of RAB6(GTP)-R6IP1 complex”. X-ray diffraction, 2 ligands (GTP, MG), 5 pockets (best druggability 0.71). MolNFT v1 #60616 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3CWZ
- Type
- protein
- Length
- 476 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-6A; RAB6-interacting protein 1
- UniProt
- P20340, Q6PAL8
- Ligands
- GTP, MG
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-6A | protein | 166 | 34% helix, 23% strand | P20340 |
| B | RAB6-interacting protein 1 | protein | 310 | 39% helix, 21% strand | Q6PAL8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.71 | 0.80 | 46 | empty |
| 2 | 246 | 0.57 | 0.78 | 46 | GTP |
| 3 | 168 | 0.48 | 0.76 | 24 | empty |
| 4 | 96 | 0.34 | 0.74 | 17 | empty |
| 5 | 88 | 0.33 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 800 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3CWZ · Structure of RAB6(GTP)-R6IP1 complex · the same entry in another collection · chain A against A, 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 0.96
- Q6PAL8 · AlphaFold monomer V2.0 prediction for denn domain-containing protein 5A (Q6PAL8) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q6PAL8
- Elsewhere: RCSB PDB 3CWZ · PDBe 3CWZ · UniProt P20340 · UniProt Q6PAL8
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