Research workbench
Complex of OxyA with the X-domain from GPA biosynthesis
Analyse Complex of OxyA with the X-domain from GPA biosynthesis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M7L
- Type
- protein
- Length
- 792 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6483
- Source
- Actinomadura parvosata subsp. kistnae
- Molecule
- Putative non-ribosomal peptide synthetase; Putative cytochrome P450 hydroxylase
- UniProt
- A0A2P9IBG7, A0A2P9IBF7
- Ligands
- HEM
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.6483 · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Putative non-ribosomal peptide synthetase | protein | 433 | 38% helix, 21% strand | A0A2P9IBG7 |
| A | Putative cytochrome P450 hydroxylase | protein | 359 | 57% helix, 9% strand | A0A2P9IBF7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.84 | 0.85 | 87 | empty |
| 2 | 597 | 0.79 | 0.84 | 76 | HEM |
| 3 | 79 | 0.72 | 0.96 | 22 | empty |
| 4 | 118 | 0.64 | 0.88 | 31 | empty |
| 5 | 167 | 0.61 | 0.84 | 22 | empty |
Interfaces
1 interface between chains.
- B–A · 1085 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6M7L · Complex of oxya with the X-domain from gpa biosynthesis · 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 A0A2P9IBG7
- Every structure of UniProt A0A2P9IBF7
- Elsewhere: RCSB PDB 6M7L · PDBe 6M7L · UniProt A0A2P9IBG7 · UniProt A0A2P9IBF7
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