MolNFT v1 · #111227 · protein
Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32W:F3Q mutant of human cellular retinoic acid binding protein II with retinal at 1.58 ångström resolution
4YKM · Cellular retinoic acid-binding protein 2: “Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32W:F3Q mutant of human cellular retinoic acid…”. X-ray diffraction, 1 ligand (RET), 4 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 4YKM
- 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 · 13% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellular retinoic acid-binding protein 2 | protein | 137 | 13% helix, 55% 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 | 283 | 0.83 | 0.94 | 38 | RET |
| 2 | 244 | 0.82 | 0.94 | 36 | RET |
| 3 | 190 | 0.50 | 0.77 | 26 | empty |
| 4 | 79 | 0.35 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 491 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 4YKM · Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32W: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 4YKM · PDBe 4YKM · UniProt P29373
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