Research workbench
Mechanistic and Structural Analysis of Substrate Recognition and Cofactor Binding by an Unusual Bacterial Prolyl Hydroxylase - Co-BaP4H-PPG
Analyse Mechanistic and Structural Analysis of Substrate Recognition and Cofactor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IAX
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Bacillus anthracis
- Molecule
- Procollagen-Proline Dioxygenase
- UniProt
- A0A0F7R8C5
- Ligands
- AKG, CO
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Procollagen-Proline Dioxygenase | protein | 199 | 22% helix, 34% strand | A0A0F7R8C5 |
| B | Procollagen-Proline Dioxygenase | protein | 194 | 22% helix, 32% strand | A0A0F7R8C5 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.63 | 0.94 | 18 | AKG |
| 2 | 113 | 0.40 | 0.76 | 24 | BME |
Interfaces
1 interface between chains.
- A–B · 1142 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5IAX · Mechanistic and structural analysis of substrate recognition and cofactor binding by an… · 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 A0A0F7R8C5
- Elsewhere: RCSB PDB 5IAX · PDBe 5IAX · UniProt A0A0F7R8C5
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