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Crystal structure of the R132K:Y134F:R111L:L121D:T54V mutant of cellular retinoic acid-binding protein II complexed with C15-aldehyde (a retinal analog) at 1.54 ångström resolution
Analyse Crystal structure of the R132K:Y134F:R111L:L121D:T54V mutant of cellular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FA6
- 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
- LSR
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellular retinoic acid-binding protein 2 | protein | 137 | 12% helix, 56% strand | P29373 |
Ligands and binding sites
- LSR · 1,3,3-trimethyl-2-[(1E,3E)-3-methylpenta-1,3-dien-1-yl]cyclohexene · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.80 | 0.87 | 43 | LSR |
| 2 | 639 | 0.80 | 0.84 | 49 | LSR |
| 3 | 76 | 0.56 | 0.88 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1028 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3FA6 · Crystal structure of the R132K:Y134F:R111L:L121D:T54V mutant of cellular retinoic… · 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 3FA6 · PDBe 3FA6 · UniProt P29373
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