MolNFT v1 · #90935 · protein
Crystal structure of ndm-1 bound to hydrolyzed meropenem
4EYL · Beta-lactamase ndm-1: “Crystal structure of ndm-1 bound to hydrolyzed meropenem”. X-ray diffraction, 2 ligands (0RV, ZN), 4 pockets (best druggability 0.79). MolNFT v1 #90935 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4EYL
- Type
- protein
- Length
- 471 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase ndm-1
- EC
- 3.5.2.6
- UniProt
- C7C422
- Ligands
- 0RV, ZN
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 231 | 27% helix, 29% strand | C7C422 |
| B | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 240 | 26% helix, 27% strand | C7C422 |
Ligands and binding sites
- 0RV · (2S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-3-methyl-2H-pyrro le-5-carboxylic acid · ligand · 2 copies · chains A, B
- ZN · Zinc 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 | 106 | 0.79 | 0.99 | 21 | empty |
| 2 | 50 | 0.31 | 0.77 | 15 | empty |
| 3 | 50 | 0.29 | 0.76 | 12 | 0RV, ZN |
| 4 | 54 | 0.27 | 0.74 | 14 | 0RV, ZN |
Interfaces
1 interface between chains.
- A–B · 954 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 4EYL · PDBe 4EYL · UniProt C7C422
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