MolNFT v1 · #105266 · protein
Crystal structure of wild type human cellular retinol binding protein II (hcrbpii) bound to retinol at 11 kev beam energy
4QZU · Retinol-binding protein 2: “Crystal structure of wild type human cellular retinol binding protein II (hcrbpii) bound to retinol at 11 kev…”. X-ray diffraction, 1 ligand (RTL), 11 pockets (best druggability 0.85). MolNFT v1 #105266…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.