Research workbench
The crystal structures of holo-and apo-cellular retinol binding protein II
Analyse The crystal structures of holo-and apo-cellular retinol binding protein II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OPB
- Type
- protein
- Length
- 532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular retinol binding protein II
- UniProt
- P06768
- Ligands
- RET
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cellular retinol binding protein II | protein | 133 | 11% helix, 56% strand | P06768 |
Ligands and binding sites
- RET · Retinal · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.83 | 0.94 | 35 | RET |
| 2 | 285 | 0.83 | 0.94 | 36 | RET |
| 3 | 277 | 0.82 | 0.93 | 35 | RET |
| 4 | 278 | 0.82 | 0.93 | 36 | RET |
| 5 | 93 | 0.57 | 0.86 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–D · 444 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 395 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 394 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1OPB · The crystal structures of holo-and apo-cellular retinol binding protein II · the same entry in another collection · chain B against B, TM-score 1.00
- P06768 · AlphaFold monomer V2.0 prediction for retinol-binding protein 2 (P06768) · a predicted model of the same protein · chain A 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 P06768
- Elsewhere: RCSB PDB 1OPB · PDBe 1OPB · UniProt P06768
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