Research workbench
Crystal structure of holo retinal-bound domain-swapped dimer of wild type human cellular retinol binding protein II
Analyse Crystal structure of holo retinal-bound domain-swapped dimer of wild type human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MCV
- Type
- protein
- Length
- 1,596 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Ligands
- RET
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Retinol-binding protein 2 | protein | 133 | 10% helix, 58% strand | P50120 |
Ligands and binding sites
- RET · Retinal · ligand · 2 copies · chains B, L, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.85 | 0.94 | 39 | empty |
| 2 | 297 | 0.85 | 0.95 | 35 | empty |
| 3 | 319 | 0.84 | 0.94 | 42 | RET |
| 4 | 291 | 0.84 | 0.95 | 39 | empty |
| 5 | 271 | 0.84 | 0.95 | 34 | empty |
Interfaces
35 interfaces between chains.
- C–G · 3920 Ų buried · 67 hydrogen bonds · protein-protein
- B–L · 3880 Ų buried · 65 hydrogen bonds · protein-protein
- E–I · 3862 Ų buried · 69 hydrogen bonds · protein-protein
- A–K · 3839 Ų buried · 69 hydrogen bonds · protein-protein
- D–H · 3830 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 6MCV · Crystal Structure of Holo Retinal-Bound Domain-Swapped Dimer of Wild Type Human Cellular… · the same entry in another collection · chain L against L, TM-score 1.00
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 P50120
- Elsewhere: RCSB PDB 6MCV · PDBe 6MCV · UniProt P50120
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