MolNFT v1 · #172234 · protein
Crystal structure of oxa-10LOOP48 in complex with hydrolyzed meropenem
6ZW2 · Beta-lactamase: “Crystal structure of oxa-10LOOP48 in complex with hydrolyzed meropenem”. X-ray diffraction, 3 ligands (8YL, CL, SO4), 5 pockets (best druggability 0.72). MolNFT v1 #172234 on GenesisL1: 3D structure, binding sites…
- PDB
- 6ZW2
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q7BNC2
- Ligands
- 8YL, CL, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 244 | 40% helix, 22% strand | Q7BNC2 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 24% strand | Q7BNC2 |
Ligands and binding sites
- 8YL · (2S,3R)-2-[(2S,3R)-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-[(3S,5S)-5-(dimethylcarbamoyl) pyrrolidin-3-yl]sulfan yl-3-methyl-2,3-dihydro-1H-pyrrole-5-carboxylic acid · ligand · 2 copies · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.72 | 0.89 | 35 | EDO |
| 2 | 101 | 0.69 | 0.92 | 26 | EDO |
| 3 | 275 | 0.56 | 0.77 | 46 | 8YL, EDO |
| 4 | 231 | 0.52 | 0.76 | 35 | CL |
| 5 | 72 | 0.38 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1319 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, carboxylation).
Compared structures
- 6ZW2 · Crystal structure of OXA-10loop48 in complex with hydrolyzed meropenem · the same entry in another collection · chain A 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 Q7BNC2
- Elsewhere: RCSB PDB 6ZW2 · PDBe 6ZW2 · UniProt Q7BNC2
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