MolNFT v2 · #141756 · protein
Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EP complex
5YPL: “Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EP complex”. X-ray diffraction at 1.8, 4 ligands (HIW, ZN, SO4). MolNFT v2 #141756 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YPL
- Type
- protein
- Length
- 458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Escherichia coli
- UniProt
- A0A0A7Y424
- Ligands
- HIW, ZN, SO4, CL
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | — | protein | 229 | — | A0A0A7Y424 |
Ligands and binding sites
- HIW · (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5YPL · Crystal structure of ndm-1 bound to hydrolyzed imipenem representing an ep complex · 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 A0A0A7Y424
- Elsewhere: RCSB PDB 5YPL · PDBe 5YPL · UniProt A0A0A7Y424
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