Research workbench
Carbapenemase VCC-1 from Vibrio cholerae N14-02106
Analyse Carbapenemase VCC-1 from Vibrio cholerae N14-02106 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MK6
- Type
- protein
- Length
- 1,042 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Vibrio cholerae
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A0U3IB62
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.7 · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 262 | 43% helix, 18% strand | A0A0U3IB62 |
| B, C, D | Beta-lactamase (EC 3.5.2.6) | protein | 260 | 43% helix, 17% strand | A0A0U3IB62 |
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.69 | 0.79 | 58 | empty |
| 2 | 498 | 0.60 | 0.74 | 70 | empty |
| 3 | 159 | 0.47 | 0.76 | 16 | empty |
| 4 | 138 | 0.45 | 0.76 | 16 | empty |
| 5 | 114 | 0.45 | 0.77 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–D · 902 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 892 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 399 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6MK6 · Carbapenemase vcc-1 from vibrio cholerae N14-02106 · 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 A0A0U3IB62
- Elsewhere: RCSB PDB 6MK6 · PDBe 6MK6 · UniProt A0A0U3IB62
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.