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The crystal structure of apo domain-swapped trimer Q108K:K40L:T51K variant of hcrbpii
Analyse The crystal structure of apo domain-swapped trimer Q108K:K40L:T51K variant of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WP1
- Type
- protein
- Length
- 798 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinol-binding protein 2
- UniProt
- P50120
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Retinol-binding protein 2 | protein | 133 | 12% helix, 56% strand | P50120 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains B, C, D, E
- ACT · Acetate ion · additive · 5 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.83 | 0.84 | 94 | empty |
| 2 | 307 | 0.82 | 0.92 | 42 | empty |
| 3 | 837 | 0.82 | 0.84 | 88 | GOL, ACT |
| 4 | 558 | 0.80 | 0.86 | 63 | GOL |
| 5 | 383 | 0.80 | 0.89 | 41 | empty |
Interfaces
11 interfaces between chains.
- B–D · 2153 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2093 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 2087 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2076 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1989 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6WP1 · The Crystal Structure of Apo Domain-Swapped Trimer Q108K:K40L:T51K Variant of HCRBPII · 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 6WP1 · PDBe 6WP1 · UniProt P50120
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