Research workbench
Crystal structure of a beta-lactamase from burkholderia phymatum
Analyse Crystal structure of a beta-lactamase from burkholderia phymatum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AO1
- Type
- protein
- Length
- 1,412 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase domain protein
- UniProt
- B2JKI6
- Ligands
- CA
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase domain protein | protein | 354 | 35% helix, 23% strand | B2JKI6 |
| B | Beta-lactamase domain protein | protein | 353 | 36% helix, 24% strand | B2JKI6 |
| C | Beta-lactamase domain protein | protein | 353 | 36% helix, 24% strand | B2JKI6 |
| D | Beta-lactamase domain protein | protein | 352 | 36% helix, 24% strand | B2JKI6 |
Ligands and binding sites
- CA · Calcium ion · metal · 17 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.83 | 0.84 | 135 | CA |
| 2 | 721 | 0.78 | 0.82 | 63 | empty |
| 3 | 703 | 0.78 | 0.82 | 59 | empty |
| 4 | 1092 | 0.77 | 0.79 | 64 | empty |
| 5 | 545 | 0.77 | 0.84 | 58 | CA |
Interfaces
5 interfaces between chains.
- C–D · 1266 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1265 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 569 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 293 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 168 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6AO1 · Crystal structure of a beta-lactamase from Burkholderia phymatum · 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 B2JKI6
- Elsewhere: RCSB PDB 6AO1 · PDBe 6AO1 · UniProt B2JKI6
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