Research workbench
Crystal structure of E. COLI mccb + ampcpp + semet mcca
Analyse Crystal structure of E. COLI mccb + ampcpp + semet mcca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H9J
- Type
- protein
- Length
- 1,360 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mccb protein; Microcin C7 analog
- UniProt
- Q47506, Q47505
- Ligands
- APC, MSE, ZN, SO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mccb protein | protein | 339 | 40% helix, 19% strand | Q47506 |
| B | Mccb protein | protein | 336 | 41% helix, 20% strand | Q47506 |
| C | Mccb protein | protein | 344 | 39% helix, 20% strand | Q47506 |
| D | Mccb protein | protein | 334 | 41% helix, 20% strand | Q47506 |
| G | Microcin C7 analog | protein | 7 | 0% helix, 0% strand | Q47505 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 5 copies · chains A, B, C, D, G
- MSE · Selenomethionine · ligand · 3 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.76 | 0.78 | 96 | MSE, APC |
| 2 | 614 | 0.72 | 0.80 | 63 | MSE, APC |
| 3 | 373 | 0.70 | 0.83 | 46 | APC |
| 4 | 280 | 0.69 | 0.84 | 42 | APC |
| 5 | 338 | 0.69 | 0.82 | 47 | empty |
Interfaces
6 interfaces between chains.
- C–D · 4413 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 4277 Ų buried · 51 hydrogen bonds · protein-protein
- C–G · 599 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 353 Ų buried · 3 hydrogen bonds · protein-protein
- D–G · 294 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (engineered).
Compared structures
- 3H9J · Crystal structure of E. coli MccB + AMPCPP + SeMeT 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 3H9J · PDBe 3H9J · UniProt Q47506 · UniProt Q47505
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