Research workbench
The crystal structure of aps domain-swapped trimer Q108K:K40D:T53A:R58L:Q38F:Q4F variant of hcrbpii
Analyse The crystal structure of aps domain-swapped trimer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VID
- Type
- protein
- Length
- 796 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 0.87
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Retinol-binding protein 2 | protein | 133 | 11% helix, 60% strand | P50120 |
| F | Retinol-binding protein 2 | protein | 131 | 8% helix, 56% strand | P50120 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, D
- ACT · Acetate ion · additive · 4 copies · chains A, D, B, E
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 | 1180 | 0.87 | 0.88 | 106 | empty |
| 2 | 325 | 0.81 | 0.91 | 39 | GOL |
| 3 | 401 | 0.80 | 0.89 | 41 | ACT |
| 4 | 587 | 0.80 | 0.85 | 61 | empty |
| 5 | 307 | 0.79 | 0.90 | 44 | GOL |
Interfaces
9 interfaces between chains.
- A–D · 2080 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2070 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 2005 Ų buried · 29 hydrogen bonds · protein-protein
- C–E · 1766 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1746 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6VID · The Crystal Structure of Aps Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F Variant… · the same entry in another collection · chain C against C, 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 0.56
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 6VID · PDBe 6VID · UniProt P50120
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