Research workbench
Crystal structure of an engineered oxa-10 variant with carbapenemase activity, oxa-10LOOP24
Analyse Crystal structure of an engineered oxa-10 variant with carbapenemase activity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QNB
- Type
- protein
- Length
- 967 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxacillinase
- EC
- 3.5.2.6
- UniProt
- Q7BNC2
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Oxacillinase (EC 3.5.2.6) | protein | 242 | 39% helix, 23% strand | Q7BNC2 |
| D | Oxacillinase (EC 3.5.2.6) | protein | 241 | 39% helix, 23% strand | Q7BNC2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.79 | 0.90 | 65 | EDO |
| 2 | 179 | 0.73 | 0.90 | 35 | EDO |
| 3 | 111 | 0.68 | 0.90 | 32 | EDO |
| 4 | 249 | 0.52 | 0.76 | 34 | SO4 |
| 5 | 223 | 0.50 | 0.76 | 34 | SO4 |
Interfaces
2 interfaces between chains.
- B–C · 1339 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1333 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, carboxylation).
Compared structures
- 3QNB · Crystal Structure of an Engineered OXA-10 Variant with 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 3QNB · PDBe 3QNB · UniProt Q7BNC2
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