Research workbench
Crystal structure of oxa-10LOOP24 in complex with ertapenem
Analyse Crystal structure of oxa-10LOOP24 in complex with ertapenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZRH
- 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
- 2RG
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 22% strand | Q7BNC2 |
| B, D | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 40% helix, 23% strand | Q7BNC2 |
Ligands and binding sites
- 2RG · (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl) carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.72 | 0.90 | 33 | EDO |
| 2 | 91 | 0.71 | 0.94 | 26 | EDO |
| 3 | 107 | 0.71 | 0.93 | 30 | EDO |
| 4 | 160 | 0.70 | 0.89 | 37 | EDO |
| 5 | 267 | 0.53 | 0.75 | 39 | 2RG |
Interfaces
2 interfaces between chains.
- B–C · 1346 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1315 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide, 4 modified (covalent ligand, disulfide, carboxylation).
Compared structures
- 6ZRH · Crystal structure of OXA-10loop24 in complex with ertapenem · 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 6ZRH · PDBe 6ZRH · UniProt Q7BNC2
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