MolNFT v1 · #65872 · protein
Crystal structure of E. COLI mccb + semet mcca
3H9Q · Mccb protein: “Crystal structure of E. COLI mccb + semet mcca”. X-ray diffraction, 3 ligands (MSE, ZN, SO4), 12 pockets (best druggability 0.73). MolNFT v1 #65872 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3H9Q
- Type
- protein
- Length
- 1,360 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mccb protein; Microcin C7 analog
- UniProt
- Q47506, Q47505
- Ligands
- MSE, ZN, SO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mccb protein | protein | 337 | 37% helix, 19% strand | Q47506 |
| B | Mccb protein | protein | 333 | 40% helix, 20% strand | Q47506 |
| C | Mccb protein | protein | 343 | 38% helix, 19% strand | Q47506 |
| D | Mccb protein | protein | 333 | 39% helix, 20% strand | Q47506 |
| E | Microcin C7 analog | protein | 5 | 0% helix, 0% strand | Q47505 |
| F | Microcin C7 analog | protein | 2 | 0% helix, 0% strand | Q47505 |
| G | Microcin C7 analog | protein | 7 | 0% helix, 0% strand | Q47505 |
Ligands and binding sites
- MSE · Selenomethionine · ligand · chains D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.73 | 0.78 | 67 | empty |
| 2 | 595 | 0.71 | 0.79 | 66 | empty |
| 3 | 526 | 0.71 | 0.80 | 70 | MSE |
| 4 | 433 | 0.65 | 0.78 | 40 | empty |
| 5 | 270 | 0.65 | 0.82 | 37 | empty |
Interfaces
11 interfaces between chains.
- C–D · 4330 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 4319 Ų buried · 51 hydrogen bonds · protein-protein
- C–G · 572 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 391 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 317 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (engineered).
Compared structures
- 3H9Q · Crystal structure of E. coli MccB + 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 3H9Q · PDBe 3H9Q · UniProt Q47506 · UniProt Q47505
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