MolNFT v1 · #23234 · protein
Crystal structure of RAB5 complex with RABAPTIN5 C-terminal domain
1TU3 · RAS-related protein rab-5A: “Crystal structure of RAB5 complex with RABAPTIN5 C-terminal domain”. X-ray diffraction, 2 ligands (GNP, MG), 17 pockets (best druggability 0.71). MolNFT v1 #23234 on GenesisL1: 3D structure, binding…
- PDB
- 1TU3
- Type
- protein
- Length
- 1,050 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-5A; Rab GTPase binding effector protein 1
- UniProt
- P20339, Q15276
- Ligands
- GNP, MG
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 10 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-5A | protein | 165 | 39% helix, 27% strand | P20339 |
| B | RAS-related protein rab-5A | protein | 166 | 38% helix, 28% strand | P20339 |
| C | RAS-related protein rab-5A | protein | 166 | 34% helix, 24% strand | P20339 |
| D | RAS-related protein rab-5A | protein | 147 | 35% helix, 19% strand | P20339 |
| E | RAS-related protein rab-5A | protein | 167 | 37% helix, 27% strand | P20339 |
| F | Rab GTPase binding effector protein 1 | protein | 46 | 85% helix, 0% strand | Q15276 |
| G | Rab GTPase binding effector protein 1 | protein | 51 | 82% helix, 0% strand | Q15276 |
| H | Rab GTPase binding effector protein 1 | protein | 44 | 77% helix, 0% strand | Q15276 |
| I | Rab GTPase binding effector protein 1 | protein | 45 | 78% helix, 0% strand | Q15276 |
| J | Rab GTPase binding effector protein 1 | protein | 53 | 70% helix, 0% strand | Q15276 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.71 | 0.82 | 32 | empty |
| 2 | 777 | 0.71 | 0.77 | 62 | empty |
| 3 | 585 | 0.69 | 0.78 | 72 | MG, GNP |
| 4 | 438 | 0.67 | 0.79 | 29 | empty |
| 5 | 233 | 0.63 | 0.82 | 21 | empty |
Interfaces
18 interfaces between chains.
- H–I · 1097 Ų buried · 4 hydrogen bonds · protein-protein
- F–G · 1076 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 539 Ų buried · 5 hydrogen bonds · protein-protein
- C–H · 529 Ų buried · 5 hydrogen bonds · protein-protein
- D–I · 523 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1TU3 · Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain · the same entry in another collection · chain J against J, 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 E against A, TM-score 0.99
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 P20339
- Every structure of UniProt Q15276
- Elsewhere: RCSB PDB 1TU3 · PDBe 1TU3 · UniProt P20339 · UniProt Q15276
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