Research workbench
Crystal structure of class D beta-lactamase oxa-48 in complex with meropenem
Analyse Crystal structure of class D beta-lactamase oxa-48 in complex with meropenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZRP
- Type
- protein
- Length
- 970 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- DWZ, CL
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 40% helix, 21% strand | Q6XEC0 |
| B, C | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- DWZ · (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.75 | 0.88 | 43 | EDO |
| 2 | 266 | 0.75 | 0.89 | 45 | empty |
| 3 | 184 | 0.68 | 0.87 | 40 | EDO |
| 4 | 513 | 0.68 | 0.78 | 47 | empty |
| 5 | 168 | 0.68 | 0.88 | 39 | EDO |
Interfaces
5 interfaces between chains.
- B–C · 793 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 529 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 528 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 249 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 246 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, carboxylation).
Compared structures
- 6ZRP · Crystal structure of class D Beta-lactamase OXA-48 in complex with 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 Q6XEC0
- Elsewhere: RCSB PDB 6ZRP · PDBe 6ZRP · UniProt Q6XEC0
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