Research workbench
Crystal structure of the Q108K:K40L:T51V:T53C:Y19W:R58W:T29L:A33W mutant of cellular retinol binding protein type II in complex with all-trans-retinal at 1.4 ångström resolution
Analyse Crystal structure of the Q108K:K40L:T51V:T53C:Y19W:R58W:T29L:A33W mutant of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EDE
- Type
- protein
- Length
- 266 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Ligands
- RET
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinol-binding protein 2 | protein | 133 | 11% helix, 54% strand | P50120 |
Ligands and binding sites
- RET · Retinal · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.85 | 0.92 | 45 | ACT, RET |
| 2 | 269 | 0.83 | 0.94 | 38 | ACT, RET |
| 3 | 90 | 0.44 | 0.79 | 26 | empty |
| 4 | 101 | 0.34 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 518 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 4EDE · Crystal Structure of the Q108K:K40L:T51V:T53C:Y19W:R58W:T29L:A33W Mutant of Cellular… · the same entry in another collection · chain A against A, TM-score 1.00
- P50120 · AlphaFold monomer V2.0 prediction for retinol-binding protein 2 (P50120) · 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 P50120
- Elsewhere: RCSB PDB 4EDE · PDBe 4EDE · UniProt P50120
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