MolNFT v1 · #172109 · protein
Crystal structure of oxa-10LOOP24 in complex with meropenem
6ZRI · Beta-lactamase: “Crystal structure of oxa-10LOOP24 in complex with meropenem”. X-ray diffraction, 1 ligand (DWZ), 8 pockets (best druggability 0.74). MolNFT v1 #172109 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZRI
- 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
- Q7BNC2
- Ligands
- DWZ
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 39% helix, 23% strand | Q7BNC2 |
| C, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 22% strand | Q7BNC2 |
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, C, B, D
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, C, B, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.74 | 0.95 | 29 | empty |
| 2 | 166 | 0.72 | 0.90 | 37 | empty |
| 3 | 99 | 0.71 | 0.93 | 27 | EDO |
| 4 | 176 | 0.70 | 0.88 | 35 | EDO |
| 5 | 243 | 0.52 | 0.76 | 40 | DWZ |
Interfaces
2 interfaces between chains.
- B–D · 1341 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1332 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide, 4 modified (covalent ligand, disulfide, carboxylation).
Compared structures
- 6ZRI · Crystal structure of OXA-10loop24 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 Q7BNC2
- Elsewhere: RCSB PDB 6ZRI · PDBe 6ZRI · UniProt Q7BNC2
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