MolNFT v1 · #107254 · protein
Crystal structure of the metallo-beta-lactamase ndm-1 in complex with a bisthiazolidine inhibitor
4U4L: “Crystal structure of the metallo-beta-lactamase ndm-1 in complex with a bisthiazolidine inhibitor”. X-ray diffraction, 2 ligands (3C7, ZN), 8 pockets (best druggability 0.73). MolNFT v1 #107254 on GenesisL1: 3D structure, binding…
- PDB
- 4U4L
- Type
- protein
- Length
- 907 residues
- Chains
- 4
- 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
- 3C7, ZN
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 229 | 24% helix, 31% strand | C7C422 |
| B | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 231 | 25% helix, 32% strand | C7C422 |
| C | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 223 | 26% helix, 30% strand | C7C422 |
| D | Beta-lactamase ndm-1 (EC 3.5.2.6) | protein | 224 | 26% helix, 30% strand | C7C422 |
Ligands and binding sites
- 3C7 · (3R,5R,7aS)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.73 | 0.77 | 96 | empty |
| 2 | 163 | 0.47 | 0.77 | 29 | empty |
| 3 | 177 | 0.42 | 0.73 | 25 | 3C7 |
| 4 | 95 | 0.39 | 0.76 | 20 | empty |
| 5 | 68 | 0.33 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–D · 438 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 401 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 285 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 177 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 49 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4U4L · Crystal structure of the metallo-beta-lactamase NDM-1 in complex with a bisthiazolidine… · the same entry in another collection · chain D against D, 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 C 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 4U4L · PDBe 4U4L · UniProt C7C422
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