MolNFT v1 · #168712 · protein
The crystal structure of domain-swapped trimer Q108K:T51D variant of hcrbpii
6WP0 · Retinol-binding protein 2: “The crystal structure of domain-swapped trimer Q108K:T51D variant of hcrbpii”. X-ray diffraction, 19 pockets (best druggability 0.87). MolNFT v1 #168712 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6WP0
- Type
- protein
- Length
- 1,596 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Retinol-binding protein 2 | protein | 133 | 11% helix, 61% strand | P50120 |
Ligands and binding sites
- GOL · Glycerol · additive · 21 copies · chains A, E, K, B, H, D, J, G, L
- ACT · Acetate ion · additive · 2 copies · chains D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.87 | 0.87 | 113 | GOL |
| 2 | 329 | 0.83 | 0.92 | 44 | empty |
| 3 | 331 | 0.83 | 0.92 | 43 | empty |
| 4 | 464 | 0.81 | 0.88 | 59 | empty |
| 5 | 798 | 0.79 | 0.82 | 98 | empty |
Interfaces
29 interfaces between chains.
- A–I · 2136 Ų buried · 34 hydrogen bonds · protein-protein
- B–J · 2073 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 2070 Ų buried · 29 hydrogen bonds · protein-protein
- F–H · 2061 Ų buried · 33 hydrogen bonds · protein-protein
- A–K · 2043 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6WP0 · The Crystal Structure of Domain-Swapped Trimer Q108K:T51D variant of HCRBPII · the same entry in another collection · chain F against F, 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 6WP0 · PDBe 6WP0 · UniProt P50120
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