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Crystal structure of class D beta-lactamase from klebsiella quasipneumoniae in complex with avibactam
Analyse Crystal structure of class D beta-lactamase from klebsiella quasipneumoniae in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XJ3
- Type
- protein
- Length
- 964 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q4LAV3
- Ligands
- NXL, CA
- Pockets
- 5 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 41% helix, 21% strand | Q4LAV3 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 41% helix, 22% strand | Q4LAV3 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 41% helix, 22% strand | Q4LAV3 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.89 | 0.91 | 176 | NXL |
| 2 | 51 | 0.67 | 0.97 | 16 | empty |
| 3 | 249 | 0.55 | 0.77 | 36 | NXL |
| 4 | 239 | 0.54 | 0.77 | 37 | NXL |
| 5 | 75 | 0.53 | 0.86 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1224 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1193 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 981 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 538 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 175 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6XJ3 · Crystal structure of Class D beta-lactamase from Klebsiella quasipneumoniae in complex… · the same entry in another collection · chain B against B, 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 Q4LAV3
- Elsewhere: RCSB PDB 6XJ3 · PDBe 6XJ3 · UniProt Q4LAV3
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