Research workbench
Crystal structure of wild type human cellular retinol binding protein II (hcrbpii) bound to retinol at 11 kev beam energy
Analyse Crystal structure of wild type human cellular retinol binding protein II… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QZU
- Type
- protein
- Length
- 532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Ligands
- RTL
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Retinol-binding protein 2 | protein | 133 | 11% helix, 56% strand | P50120 |
Ligands and binding sites
- RTL · Retinol · ligand · 3 copies · chains A, C, B
- ACT · Acetate ion · additive · 6 copies · chains A, C, B, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.85 | 0.97 | 32 | RTL, GOL |
| 2 | 282 | 0.85 | 0.95 | 40 | empty |
| 3 | 250 | 0.84 | 0.96 | 33 | RTL, ACT |
| 4 | 460 | 0.82 | 0.89 | 66 | RTL, ACT |
| 5 | 224 | 0.72 | 0.87 | 39 | empty |
Interfaces
5 interfaces between chains.
- B–D · 576 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 537 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 515 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 435 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 290 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QZU · Crystal Structure of wild type Human Cellular Retinol Binding Protein II (hCRBPII) bound… · 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 0.99
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 4QZU · PDBe 4QZU · UniProt P50120
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