MolNFT v1 · #189204 · protein
Crystal structure of human osbp ord in complex with cholesterol
7V62 · Oxysterol-binding protein 1: “Crystal structure of human osbp ord in complex with cholesterol”. X-ray diffraction, 1 ligand (CLR), 19 pockets (best druggability 0.85). MolNFT v1 #189204 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7V62
- Type
- protein
- Length
- 1,547 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterol-binding protein 1
- UniProt
- P22059
- Ligands
- CLR
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterol-binding protein 1 | protein | 390 | 27% helix, 32% strand | P22059 |
| B, D | Oxysterol-binding protein 1 | protein | 384 | 25% helix, 32% strand | P22059 |
| C | Oxysterol-binding protein 1 | protein | 389 | 27% helix, 32% strand | P22059 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 4 copies · chains A, B, C, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 6 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, C, D
- CIT · Citric acid · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.85 | 0.88 | 97 | DMS |
| 2 | 531 | 0.85 | 0.90 | 58 | CLR |
| 3 | 668 | 0.84 | 0.87 | 75 | CLR |
| 4 | 766 | 0.83 | 0.87 | 96 | CIT |
| 5 | 583 | 0.83 | 0.88 | 61 | CLR |
Interfaces
5 interfaces between chains.
- B–C · 1105 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1105 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 729 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 599 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 561 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 covalent (disulfide, additive adduct).
Compared structures
- 7V62 · Crystal structure of human OSBP ORD in complex with cholesterol · the same entry in another collection · chain A against A, TM-score 1.00
- P22059 · AlphaFold monomer V2.0 prediction for oxysterol-binding protein 1 (P22059) · a predicted model of the same protein · chain B 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 P22059
- Elsewhere: RCSB PDB 7V62 · PDBe 7V62 · UniProt P22059
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