Research workbench
Crystal structure of ndm-1 beta-lactamase in complex with boronic inhibitor cpd 6
Analyse Crystal structure of ndm-1 beta-lactamase in complex with boronic inhibitor cpd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IBS
- Type
- protein
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase type 2
- EC
- 3.5.2.6
- UniProt
- C7C422
- Ligands
- HB8, ZN, CA
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 225 | 27% helix, 29% strand | C7C422 |
| B | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 228 | 26% helix, 30% strand | C7C422 |
Ligands and binding sites
- HB8 · [7-[(2-methylpropan-2-yl)oxycarbonylamino]-1-benzothiophen-2-yl]-tris(oxidanyl)boranuide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.79 | 0.99 | 21 | empty |
| 2 | 79 | 0.45 | 0.82 | 21 | empty |
| 3 | 67 | 0.31 | 0.75 | 21 | empty |
| 4 | 64 | 0.29 | 0.74 | 20 | HB8 |
Interfaces
1 interface between chains.
- A–B · 936 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6IBS · Crystal structure of NDM-1 beta-lactamase in complex with boronic inhibitor cpd 6 · the same entry in another collection · chain A against A, TM-score 1.00
- C7C422 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (C7C422) · a predicted model of the same protein · 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 C7C422
- Elsewhere: RCSB PDB 6IBS · PDBe 6IBS · UniProt C7C422
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