Research workbench
Crystal structure of pena beta-lactamase-avibactam complex
Analyse Crystal structure of pena beta-lactamase-avibactam complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DOO
- Type
- protein
- Length
- 780 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A0H3KN52
- Ligands
- NXL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-lactamase (EC 3.5.2.6) | protein | 260 | 43% helix, 18% strand | A0A0H3KN52 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.78 | 0.80 | 102 | empty |
| 2 | 317 | 0.56 | 0.76 | 32 | empty |
| 3 | 252 | 0.52 | 0.76 | 47 | NXL |
| 4 | 82 | 0.50 | 0.83 | 20 | empty |
| 5 | 193 | 0.49 | 0.76 | 32 | NXL |
Interfaces
3 interfaces between chains.
- A–C · 523 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 417 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 285 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7DOO · Crystal Structure of PenA beta-Lactamase-Avibactam Complex · 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 A0A0H3KN52
- Elsewhere: RCSB PDB 7DOO · PDBe 7DOO · UniProt A0A0H3KN52
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