Research workbench
The structure of microcin C7 biosynthetic enzyme mccb in complex with N-formylated mcca
Analyse The structure of microcin C7 biosynthetic enzyme mccb in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OM4
- Type
- protein
- Length
- 703 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mccb protein; Microcin C7
- UniProt
- Q47506, Q47505
- Ligands
- POP, ND7, MG, ZN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mccb protein | protein | 345 | 40% helix, 20% strand | Q47506 |
| B | Mccb protein | protein | 344 | 40% helix, 20% strand | Q47506 |
| C, D | Microcin C7 | protein | 7 | 0% helix, 14% strand | Q47505 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- ND7 · 5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine · ligand · 2 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.66 | 0.80 | 42 | MG, POP, ND7 |
| 2 | 357 | 0.65 | 0.80 | 44 | POP, MG, ND7 |
| 3 | 83 | 0.41 | 0.79 | 22 | empty |
| 4 | 64 | 0.37 | 0.79 | 18 | empty |
| 5 | 79 | 0.30 | 0.73 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 4763 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 673 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 638 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 295 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 261 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, formylation).
Compared structures
- 6OM4 · The structure of Microcin C7 biosynthetic enzyme MccB in complex with N-formylated MccA · 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 Q47506
- Every structure of UniProt Q47505
- Elsewhere: RCSB PDB 6OM4 · PDBe 6OM4 · UniProt Q47506 · UniProt Q47505
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