MolNFT v1 · #94049 · protein
New delhi metallo-beta-lactamase-1, complexed with CD and faropenem
4HKY · Beta-lactamase ndm-1: “New delhi metallo-beta-lactamase-1, complexed with CD and faropenem”. X-ray diffraction, 4 ligands (FPM, SFR, CD), 5 pockets (best druggability 0.75). MolNFT v1 #94049 on GenesisL1: 3D structure, binding sites…
- PDB
- 4HKY
- Type
- protein
- Length
- 469 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
- FPM, SFR, CD, CL
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 228 | 26% helix, 30% strand | C7C422 |
| B | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 241 | 26% helix, 31% strand | C7C422 |
Ligands and binding sites
- FPM · (5R,6S)-6-(1-hydroxyethyl)-7-oxo-3-[(2R)-oxolan-2-yl]-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid · ligand · 2 copies · chains A, B
- SFR · (2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · 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 | 99 | 0.75 | 0.96 | 21 | empty |
| 2 | 181 | 0.44 | 0.74 | 29 | SFR, FPM, CD, CL |
| 3 | 76 | 0.43 | 0.81 | 17 | empty |
| 4 | 69 | 0.29 | 0.73 | 12 | FPM, SFR, CD |
| 5 | 52 | 0.27 | 0.74 | 15 | CL |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4HKY · New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem · 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 4HKY · PDBe 4HKY · UniProt C7C422
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.