Research workbench
Crystal structure of NDM-1 in complex with D-captopril derivative wss0218
Analyse Crystal structure of NDM-1 in complex with D-captopril derivative wss0218 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LIP
- Type
- protein
- Length
- 229 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 0.98
- Source
- Klebsiella pneumoniae
- Molecule
- Metallo-beta-lactamase type 2
- EC
- 3.5.2.6
- UniProt
- C7C422
- Ligands
- EEL, ZN
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · resolution 0.98 · 1 distinct chain · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 229 | 25% helix, 30% strand | C7C422 |
Ligands and binding sites
- EEL · (2R)-1-[3-sulfanyl-2-(sulfanylmethyl) propanoyl]pyrrolidine-2-carboxylic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.32 | 0.75 | 15 | ZN, EEL |
Compared structures
- 6LIP · Crystal structure of ndm-1 in complex with D-captopril derivative WSS0218 · 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 0.99
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 6LIP · PDBe 6LIP · UniProt C7C422
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