Research workbench
Crystal structure of ndm-1 metallo-beta-lactamase in complex with CD ions and a hydrolyzed beta-lactam ligand - new refinement
Analyse Crystal structure of ndm-1 metallo-beta-lactamase in complex with CD ions and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EX7
- Type
- protein
- Length
- 481 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
- UNL, TOE, CD, CL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 240 | 26% helix, 32% strand | C7C422 |
| B | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 241 | 26% helix, 32% strand | C7C422 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- TOE · 2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxyl · ligand · chains B
- CD · Cadmium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.76 | 0.97 | 20 | empty |
| 2 | 82 | 0.44 | 0.80 | 18 | empty |
| 3 | 77 | 0.38 | 0.78 | 18 | empty |
| 4 | 92 | 0.36 | 0.75 | 24 | CD, UNL |
| 5 | 96 | 0.35 | 0.74 | 20 | CD, UNL |
Interfaces
1 interface between chains.
- A–B · 920 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6EX7 · Crystal structure of NDM-1 metallo-beta-lactamase in complex with Cd ions and a… · 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 0.95
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 6EX7 · PDBe 6EX7 · UniProt C7C422
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