MolNFT v1 · #153625 · protein
Crystal structure of metallo-beta-lactamse, imp-1, in complex with a thiazole-bearing inhibitor
6JKA · Metallo-beta-lactamase type 2: “Crystal structure of metallo-beta-lactamse, imp-1, in complex with a thiazole-bearing inhibitor”. X-ray diffraction, 3 ligands (BS0, BQU, ZN), 12 pockets (best druggability 0.76). MolNFT v1 #153625 on…
- PDB
- 6JKA
- Type
- protein
- Length
- 895 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallo-beta-lactamase type 2
- EC
- 3.5.2.6
- UniProt
- P52699
- Ligands
- BS0, BQU, ZN
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 227 | 27% helix, 29% strand | P52699 |
| B | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 220 | 27% helix, 32% strand | P52699 |
| C | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 228 | 27% helix, 30% strand | P52699 |
| D | Metallo-beta-lactamase type 2 (EC 3.5.2.6) | protein | 220 | 28% helix, 31% strand | P52699 |
Ligands and binding sites
- BS0 · 6-[2-(phenoxymethyl)-1,3-thiazol-4-yl]-3,4-dihydro-1H-quinolin-2-one · ligand · 2 copies · chains A, C
- BQU · 3-[2-azanyl-5-[2-(phenoxymethyl)-1,3-thiazol-4-yl]phenyl]propanoic acid · ligand · chains B, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.76 | 0.84 | 52 | BQU |
| 2 | 560 | 0.74 | 0.82 | 69 | BS0 |
| 3 | 345 | 0.63 | 0.79 | 37 | empty |
| 4 | 260 | 0.58 | 0.78 | 30 | empty |
| 5 | 223 | 0.56 | 0.78 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–C · 770 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 683 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 444 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6JKA · Crystal structure of metallo-beta-lactamse, IMP-1, in complex with a thiazole-bearing… · the same entry in another collection · chain D against D, TM-score 1.00
- P52699 · AlphaFold monomer V2.0 prediction for metallo-beta-lactamase type 2 (P52699) · a predicted model of the same protein · chain B 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 P52699
- Elsewhere: RCSB PDB 6JKA · PDBe 6JKA · UniProt P52699
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