Research workbench
Crystal structure of putative asparaginyl hydroxylase (2636534) from bacillus subtilis at 2.60 a resolution
Analyse Crystal structure of putative asparaginyl hydroxylase (2636534) from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VRB
- Type
- protein
- Length
- 1,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative asparaginyl hydroxylase
- UniProt
- P46327
- Ligands
- FE
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative asparaginyl hydroxylase | protein | 302 | 38% helix, 21% strand | P46327 |
| B | Putative asparaginyl hydroxylase | protein | 311 | 38% helix, 23% strand | P46327 |
| C | Putative asparaginyl hydroxylase | protein | 298 | 40% helix, 20% strand | P46327 |
| D | Putative asparaginyl hydroxylase | protein | 313 | 38% helix, 21% strand | P46327 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.79 | 0.81 | 88 | FE |
| 2 | 745 | 0.78 | 0.82 | 86 | FE |
| 3 | 317 | 0.69 | 0.83 | 45 | FE |
| 4 | 320 | 0.65 | 0.80 | 34 | FE |
| 5 | 372 | 0.61 | 0.77 | 48 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3307 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 3248 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 406 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1VRB · Crystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at… · the same entry in another collection · chain D against D, TM-score 1.00
- P46327 · AlphaFold monomer V2.0 prediction for uncharacterized protein yxbc (P46327) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P46327
- Elsewhere: RCSB PDB 1VRB · PDBe 1VRB · UniProt P46327
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