MolNFT v1 · #168714 · protein
The crystal structure of apo zinc-bound domain swapped-trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H variant of hcrbpii
6WP2 · Retinol-binding protein 2: “The crystal structure of apo zinc-bound domain swapped-trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H variant of…”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.82). MolNFT v1 #168714 on…
- PDB
- 6WP2
- Type
- protein
- Length
- 399 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Retinol-binding protein 2 | protein | 133 | 10% helix, 59% strand | P50120 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- ACT · Acetate ion · additive · chains C
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 | 352 | 0.82 | 0.91 | 39 | empty |
| 2 | 405 | 0.79 | 0.88 | 55 | ACT |
| 3 | 434 | 0.78 | 0.87 | 53 | ZN, GOL |
| 4 | 83 | 0.37 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2090 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2045 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2038 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6WP2 · The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer… · 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 P50120
- Elsewhere: RCSB PDB 6WP2 · PDBe 6WP2 · UniProt P50120
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