MolNFT v1 · #161153 · protein
Oxa-48_P68A-avi. evolutionary trade-offs of oxa-48 mediated ceftazidime-avibactam resistance
6Q5B · Beta-lactamase: “Oxa-48_P68A-avi. evolutionary trade-offs of oxa-48 mediated ceftazidime-avibactam resistance”. X-ray diffraction, 4 ligands (NXL, CL, CO2), 7 pockets (best druggability 0.78). MolNFT v1 #161153 on GenesisL1: 3D…
- PDB
- 6Q5B
- Type
- protein
- Length
- 948 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- NXL, CL, CO2, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 233 | 39% helix, 24% strand | Q6XEC0 |
| B, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 21% strand | Q6XEC0 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 231 | 41% helix, 23% strand | Q6XEC0 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- CO2 · Carbon dioxide · ion · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.78 | 0.80 | 136 | NXL, CO2, CL |
| 2 | 849 | 0.78 | 0.81 | 117 | NXL, CL, SO4 |
| 3 | 126 | 0.43 | 0.76 | 20 | CO2 |
| 4 | 53 | 0.36 | 0.79 | 16 | empty |
| 5 | 58 | 0.35 | 0.78 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1011 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 980 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, carboxylation).
Compared structures
- 6Q5B · OXA-48_P68A-AVI. Evolutionary trade-offs of OXA-48 mediated ceftazidime-avibactam… · 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 6Q5B · PDBe 6Q5B · UniProt Q6XEC0
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