MolNFT v1 · #152938 · protein
Structure of human ORP1 ank - RAB7 complex
6IYB · RAS-related protein rab-7A: “Structure of human ORP1 ank - RAB7 complex”. X-ray diffraction, 2 ligands (GTP, MG), 5 pockets (best druggability 0.78). MolNFT v1 #152938 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IYB
- Type
- protein
- Length
- 612 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-7A; Oxysterol-binding protein-related protein 1
- UniProt
- P51149, Q9BXW6
- Ligands
- GTP, MG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RAS-related protein rab-7A | protein | 171 | 36% helix, 26% strand | P51149 |
| B | Oxysterol-binding protein-related protein 1 | protein | 135 | 54% helix, 1% strand | Q9BXW6 |
| D | Oxysterol-binding protein-related protein 1 | protein | 135 | 53% helix, 1% strand | Q9BXW6 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, 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 | 861 | 0.78 | 0.81 | 82 | empty |
| 2 | 159 | 0.53 | 0.80 | 30 | MG, GTP |
| 3 | 159 | 0.52 | 0.79 | 30 | MG, GTP |
| 4 | 144 | 0.40 | 0.73 | 28 | empty |
| 5 | 57 | 0.32 | 0.76 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 721 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 719 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 392 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 370 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 66 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6IYB · Structure of human ORP1 ANK - Rab7 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P51149 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-7A (P51149) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9BXW6 · AlphaFold monomer V2.0 prediction for oxysterol-binding protein- related protein 1… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P51149
- Every structure of UniProt Q9BXW6
- Elsewhere: RCSB PDB 6IYB · PDBe 6IYB · UniProt P51149 · UniProt Q9BXW6
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