Research workbench
Crystal structure of the class D beta-lactamase oxa-935 from pseudomonas aeruginosa, orthorhombic crystal form
Analyse Crystal structure of the class D beta-lactamase oxa-935 from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N1M
- Type
- protein
- Length
- 477 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase oxa-935
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase oxa-935 | protein | 241 | 40% helix, 24% strand | — |
| B | Beta-lactamase oxa-935 | protein | 236 | 40% helix, 24% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 22 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.70 | 0.89 | 30 | empty |
| 2 | 129 | 0.70 | 0.90 | 32 | empty |
| 3 | 146 | 0.50 | 0.79 | 29 | SO4 |
| 4 | 147 | 0.43 | 0.75 | 25 | SO4 |
| 5 | 65 | 0.36 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1252 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7N1M · Crystal Structure of the Class D Beta-lactamase OXA-935 from Pseudomonas aeruginosa… · 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
- Elsewhere: RCSB PDB 7N1M · PDBe 7N1M
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