Research workbench
High resolution structure of acinetobacter baumannii beta-lactamase oxa-51
Analyse High resolution structure of acinetobacter baumannii beta-lactamase oxa-51 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KZH
- Type
- protein
- Length
- 960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q5QT35
- Pockets
- 9 · best druggability 0.75
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 | 240 | 41% helix, 22% strand | Q5QT35 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 239 | 41% helix, 21% strand | Q5QT35 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 241 | 41% helix, 22% strand | Q5QT35 |
Ligands and binding sites
- FMT · Formic acid · additive · 7 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 5 copies · chains A, B, C, D
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 | 562 | 0.75 | 0.82 | 79 | empty |
| 2 | 388 | 0.71 | 0.82 | 43 | empty |
| 3 | 191 | 0.53 | 0.78 | 30 | FMT, ACT |
| 4 | 170 | 0.49 | 0.77 | 30 | FMT, ACT |
| 5 | 164 | 0.48 | 0.76 | 28 | FMT |
Interfaces
5 interfaces between chains.
- B–D · 425 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 399 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 384 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 345 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5KZH · High Resolution Structure of Acinetobacter baumannii beta-lactamase OXA-51 · 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 Q5QT35
- Elsewhere: RCSB PDB 5KZH · PDBe 5KZH · UniProt Q5QT35
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