Research workbench
Crystal structure of the Q108K:K40L:T51V:R58F mutant of human cellular retinol binding protein II in complex with synthetic ligand julolidine
Analyse Crystal structure of the Q108K:K40L:T51V:R58F mutant of human cellular retinol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C7Z
- 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
- JLO
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinol-binding protein 2 | protein | 133 | 11% helix, 56% strand | P50120 |
Ligands and binding sites
- JLO · (2E,4E)-3-methyl-5-(2,3,6,7-tetrahydro-1H,5H-pyrido[3, 2,1-ij]quinolin-9-yl)penta-2,4-dienal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.84 | 0.94 | 39 | ACT, JLO |
| 2 | 270 | 0.82 | 0.93 | 37 | ACT, JLO |
| 3 | 249 | 0.52 | 0.75 | 30 | empty |
| 4 | 56 | 0.33 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 600 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6C7Z · Crystal structure of the Q108K:K40L:T51V:R58F mutant of human Cellular Retinol Binding… · 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 6C7Z · PDBe 6C7Z · UniProt P50120
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