Research workbench
Crystal structure of E. COLI mccb + mcca-N7ISOASN
Analyse Crystal structure of E. COLI mccb + mcca-N7ISOASN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H9G
- Type
- protein
- Length
- 1,397 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mccb protein; Microcin C7 analog
- UniProt
- Q47506, Q47505
- Ligands
- ZN, SO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mccb protein | protein | 346 | 38% helix, 19% strand | Q47506 |
| B, D | Mccb protein | protein | 340 | 41% helix, 20% strand | Q47506 |
| C | Mccb protein | protein | 345 | 39% helix, 19% strand | Q47506 |
| E, F, H | Microcin C7 analog | protein | 7 | 0% helix, 14% strand | Q47505 |
| G | Microcin C7 analog | protein | 5 | 0% helix, 0% strand | Q47505 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.77 | 0.79 | 90 | empty |
| 2 | 482 | 0.71 | 0.81 | 66 | SO4 |
| 3 | 439 | 0.68 | 0.80 | 67 | SO4 |
| 4 | 375 | 0.67 | 0.81 | 50 | SO4 |
| 5 | 376 | 0.65 | 0.80 | 59 | SO4 |
Interfaces
12 interfaces between chains.
- A–B · 4661 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 4590 Ų buried · 57 hydrogen bonds · protein-protein
- B–F · 662 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 657 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 632 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 3H9G · Crystal structure of E. coli MccB + MccA-N7isoASN · 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 3H9G · PDBe 3H9G · UniProt Q47506 · UniProt Q47505
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