MolNFT v1 · #172110 · protein
Crystal structure of class D beta-lactamase oxa-48 in complex with ertapenem
6ZRJ: “Crystal structure of class D beta-lactamase oxa-48 in complex with ertapenem”. X-ray diffraction, 2 ligands (2RG, CL), 13 pockets (best druggability 0.80). MolNFT v1 #172110 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6ZRJ
- Type
- protein
- Length
- 1,939 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- 2RG, CL
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 40% helix, 21% strand | Q6XEC0 |
| D, E, F, G, H | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 20% strand | Q6XEC0 |
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 · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B, C, D, F, G, H
- PGE · Triethylene glycol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.80 | 0.82 | 121 | empty |
| 2 | 909 | 0.79 | 0.81 | 125 | 2RG, EDO, CL |
| 3 | 991 | 0.78 | 0.80 | 125 | 2RG, EDO, PGE |
| 4 | 917 | 0.78 | 0.81 | 123 | 2RG, EDO |
| 5 | 113 | 0.41 | 0.76 | 26 | empty |
Interfaces
8 interfaces between chains.
- C–D · 991 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 977 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 973 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 972 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 289 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 7 modified (covalent ligand, carboxylation).
Compared structures
- 6ZRJ · Crystal structure of class D Beta-lactamase OXA-48 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 Q6XEC0
- Elsewhere: RCSB PDB 6ZRJ · PDBe 6ZRJ · UniProt Q6XEC0
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