MolNFT v1 · #104419 · protein
Crystal structure of the RAB5, rabex-5DELTA and rabaptin-5C21 complex
4Q9U · RAB5 GDP/GTP exchange factor: “Crystal structure of the RAB5, rabex-5DELTA and rabaptin-5C21 complex”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #104419 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4Q9U
- Type
- protein
- Length
- 1,196 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAB5 GDP/GTP exchange factor; RAS-related protein rab-5A; Rab GTPase-binding effector…
- UniProt
- Q9UJ41, P20339, Q15276
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAB5 GDP/GTP exchange factor | protein | 303 | 72% helix, 0% strand | Q9UJ41 |
| B | RAS-related protein rab-5A | protein | 153 | 31% helix, 18% strand | P20339 |
| C | Rab GTPase-binding effector protein 1 | protein | 83 | 92% helix, 0% strand | Q15276 |
| D | Rab GTPase-binding effector protein 1 | protein | 75 | 96% helix, 0% strand | Q15276 |
| E | RAB5 GDP/GTP exchange factor | protein | 296 | 75% helix, 0% strand | Q9UJ41 |
| F | RAS-related protein rab-5A | protein | 120 | 33% helix, 18% strand | P20339 |
| G | Rab GTPase-binding effector protein 1 | protein | 84 | 89% helix, 0% strand | Q15276 |
| H | Rab GTPase-binding effector protein 1 | protein | 82 | 95% helix, 0% strand | Q15276 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.86 | 0.87 | 113 | empty |
| 2 | 1125 | 0.84 | 0.84 | 98 | empty |
| 3 | 1015 | 0.82 | 0.83 | 102 | empty |
| 4 | 825 | 0.80 | 0.82 | 69 | empty |
| 5 | 135 | 0.79 | 0.96 | 27 | empty |
Interfaces
18 interfaces between chains.
- E–H · 1628 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1406 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 1357 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1255 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1150 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4Q9U · Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex · the same entry in another collection · chain H against H, TM-score 1.00
- P20339 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-5A (P20339) · a predicted model of the same protein · chain B against A, TM-score 0.91
- Q15276 · AlphaFold monomer V2.0 prediction for rab GTPase-binding effector protein 1 (Q15276) · a predicted model of the same protein · chain H against A, TM-score 0.86
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 Q9UJ41
- Every structure of UniProt P20339
- Every structure of UniProt Q15276
- Elsewhere: RCSB PDB 4Q9U · PDBe 4Q9U · UniProt Q9UJ41 · UniProt P20339 · UniProt Q15276
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