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The crystal structure of apo domain-swapped trimer Q108K:T51D:A28C:I32C of hcrbpii
Analyse The crystal structure of apo domain-swapped trimer Q108K:T51D:A28C:I32C of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WNJ
- 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
- SO4
- Pockets
- 4 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Retinol-binding protein 2 | protein | 133 | 11% helix, 59% strand | P50120 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B, C
- 144 · Tris-hydroxymethyl-methyl-ammonium · additive · 3 copies · chains A, B, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.90 | 0.92 | 134 | GOL, 144 |
| 2 | 129 | 0.37 | 0.73 | 23 | empty |
| 3 | 112 | 0.36 | 0.74 | 16 | empty |
| 4 | 74 | 0.30 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2123 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2110 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2103 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6WNJ · The Crystal Structure of Apo Domain-Swapped Trimer Q108K:T51D:A28C:I32C 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 6WNJ · PDBe 6WNJ · UniProt P50120
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