MolNFT v1 · #111229 · protein
Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32Y:F3Q mutant of human cellular retinoic acid binding protein II with retinal at 1.58 ångström resolution
4YKO · Cellular retinoic acid-binding protein 2: “Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32Y:F3Q mutant of human cellular retinoic acid…”. X-ray diffraction, 1 ligand (RET), 4 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 4YKO
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular retinoic acid-binding protein 2
- UniProt
- P29373
- Ligands
- RET
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellular retinoic acid-binding protein 2 | protein | 137 | 14% helix, 53% strand | P29373 |
Ligands and binding sites
- RET · Retinal · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.83 | 0.95 | 30 | RET |
| 2 | 261 | 0.82 | 0.93 | 29 | RET |
| 3 | 196 | 0.50 | 0.77 | 31 | empty |
| 4 | 84 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 471 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 4YKO · Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32Y:F3Q mutant of human… · the same entry in another collection · chain A against A, 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 P29373
- Elsewhere: RCSB PDB 4YKO · PDBe 4YKO · UniProt P29373
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