Research workbench
Crystal structure of a beta-lactamase domain protein from burkholderia ambifaria
Analyse Crystal structure of a beta-lactamase domain protein from burkholderia ambifaria in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I0P
- Type
- protein
- Length
- 1,328 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase domain protein
- UniProt
- B1YNR3
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase domain protein | protein | 322 | 33% helix, 25% strand | B1YNR3 |
| B | Beta-lactamase domain protein | protein | 323 | 33% helix, 25% strand | B1YNR3 |
| C | Beta-lactamase domain protein | protein | 339 | 33% helix, 25% strand | B1YNR3 |
| D | Beta-lactamase domain protein | protein | 344 | 35% helix, 24% strand | B1YNR3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.78 | 0.79 | 79 | empty |
| 2 | 720 | 0.72 | 0.78 | 68 | empty |
| 3 | 597 | 0.69 | 0.78 | 65 | empty |
| 4 | 385 | 0.65 | 0.79 | 45 | empty |
| 5 | 339 | 0.60 | 0.78 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1258 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1238 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 507 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5I0P · Crystal Structure of a Beta-lactamase domain protein from Burkholderia ambifaria · 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 B1YNR3
- Elsewhere: RCSB PDB 5I0P · PDBe 5I0P · UniProt B1YNR3
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