MolNFT v1 · #93317 · protein
Crystal structure of new delhi metallo-beta-lactamase-1 A121F mutant from klebsiella pneumoniae
4GYU · Beta-lactamase ndm-1: “Crystal structure of new delhi metallo-beta-lactamase-1 A121F mutant from klebsiella pneumoniae”. X-ray diffraction, 3 pockets (best druggability 0.70). MolNFT v1 #93317 on GenesisL1: 3D structure, binding…
- PDB
- 4GYU
- Type
- protein
- Length
- 241 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase ndm-1
- EC
- 3.5.2.6
- UniProt
- C7C422
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 241 | 23% helix, 29% strand | C7C422 |
Ligands and binding sites
- IMD · Imidazole · additive · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- P6G · Hexaethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.70 | 0.98 | 18 | IMD |
| 2 | 256 | 0.55 | 0.77 | 32 | empty |
| 3 | 57 | 0.28 | 0.74 | 16 | P6G |
Compared structures
- 4GYU · Crystal Structure of New Delhi Metallo-beta-Lactamase-1 A121F mutant from Klebsiella… · 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 0.94
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 4GYU · PDBe 4GYU · UniProt C7C422
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