Research workbench
Mechanistic and Structural Analysis of Substrate Recognition and Cofactor Binding by an Unusual Bacterial Prolyl Hydroxylase - apo-BaP4H
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
- 5IAT
- Type
- protein
- Length
- 401 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.67
- Source
- Bacillus anthracis
- Molecule
- Procollagen-Proline Dioxygenase
- UniProt
- A0A0F7R8C5
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · resolution 1.67 · 2 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Procollagen-Proline Dioxygenase | protein | 206 | 20% helix, 30% strand | A0A0F7R8C5 |
| B | Procollagen-Proline Dioxygenase | protein | 195 | 21% helix, 31% strand | A0A0F7R8C5 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · 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 | 138 | 0.58 | 0.83 | 30 | empty |
| 2 | 105 | 0.56 | 0.84 | 20 | empty |
| 3 | 112 | 0.41 | 0.76 | 23 | empty |
| 4 | 53 | 0.27 | 0.74 | 13 | GOL |
Interfaces
1 interface between chains.
- A–B · 1172 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5IAT · 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 5IAT · PDBe 5IAT · UniProt A0A0F7R8C5
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