MolNFT v1 · #76519 · protein
Crystal structure of a rationally designed oxa-10 variant showing carbapenemase activity, oxa-10LOOP48
3QNC · Oxacillinase: “Crystal structure of a rationally designed oxa-10 variant showing carbapenemase activity, oxa-10LOOP48”. X-ray diffraction, 2 ligands (SO4, CO2), 6 pockets (best druggability 0.72). MolNFT v1 #76519 on GenesisL1: 3D…
- PDB
- 3QNC
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxacillinase
- EC
- 3.5.2.6
- UniProt
- Q7BNC2
- Ligands
- SO4, CO2
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxacillinase (EC 3.5.2.6) | protein | 242 | 39% helix, 23% strand | Q7BNC2 |
| B | Oxacillinase (EC 3.5.2.6) | protein | 243 | 37% helix, 24% strand | Q7BNC2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B
- CO2 · Carbon dioxide · ion · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.72 | 0.90 | 31 | SO4 |
| 2 | 172 | 0.68 | 0.87 | 33 | EDO |
| 3 | 220 | 0.49 | 0.75 | 33 | SO4 |
| 4 | 210 | 0.48 | 0.75 | 34 | SO4 |
| 5 | 62 | 0.34 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1276 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, carboxylation).
Compared structures
- 3QNC · Crystal Structure of a Rationally Designed OXA-10 Variant Showing Carbapenemase Activity… · 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 3QNC · PDBe 3QNC · UniProt Q7BNC2
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