Research workbench
Structure of ORP1L/RAB7 complex
Analyse Structure of ORP1L/RAB7 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z2M
- Type
- protein
- Length
- 613 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterol-binding protein-related protein 1; RAS-related protein rab-7A
- UniProt
- Q91XL9, P51150
- Ligands
- GTP, MG
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Oxysterol-binding protein-related protein 1 | protein | 137 | 52% helix, 1% strand | Q91XL9 |
| A | RAS-related protein rab-7A | protein | 172 | 35% helix, 26% strand | P51150 |
| C | RAS-related protein rab-7A | protein | 168 | 36% helix, 24% strand | P51150 |
| D | Oxysterol-binding protein-related protein 1 | protein | 136 | 51% helix, 1% strand | Q91XL9 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.59 | 0.76 | 48 | MG, GTP |
| 2 | 165 | 0.52 | 0.79 | 27 | GTP |
| 3 | 123 | 0.43 | 0.77 | 21 | empty |
| 4 | 141 | 0.42 | 0.75 | 26 | empty |
| 5 | 53 | 0.31 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–D · 730 Ų buried · 20 hydrogen bonds · protein-protein
- B–A · 515 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 431 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5Z2M · Structure of Orp1L/Rab7 complex · the same entry in another collection · chain D against D, TM-score 1.00
- P51150 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-7A (P51150) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q91XL9 · AlphaFold monomer V2.0 prediction for oxysterol-binding protein- related protein 1… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q91XL9
- Every structure of UniProt P51150
- Elsewhere: RCSB PDB 5Z2M · PDBe 5Z2M · UniProt Q91XL9 · UniProt P51150
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