Research workbench
Structural analysis of cofactor binding of a prolyl 4-hydroxylase from the pathogenic bacterium bacillus anthracis
Analyse Structural analysis of cofactor binding of a prolyl 4-hydroxylase from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HV0
- Type
- protein
- Length
- 403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl 4-hydroxylase
- UniProt
- Q81LZ8
- Ligands
- AKG, CD, K
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl 4-hydroxylase | protein | 206 | 18% helix, 33% strand | Q81LZ8 |
| B | Prolyl 4-hydroxylase | protein | 197 | 20% helix, 32% strand | Q81LZ8 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 14 copies · chains A, B
- K · Potassium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.63 | 0.90 | 27 | CD, AKG |
| 2 | 62 | 0.60 | 0.91 | 19 | CD, AKG |
| 3 | 139 | 0.42 | 0.75 | 26 | GOL |
| 4 | 57 | 0.25 | 0.72 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1126 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5HV0 · Structural Analysis of Cofactor Binding of a Prolyl 4-Hydroxylase from the Pathogenic… · 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 Q81LZ8
- Elsewhere: RCSB PDB 5HV0 · PDBe 5HV0 · UniProt Q81LZ8
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