Research workbench
The crystal structure of a class D beta-lactamase from agrobacterium tumefaciens
Analyse The crystal structure of a class D beta-lactamase from agrobacterium tumefaciens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V6N
- Type
- protein
- Length
- 986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A1V2APZ1
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 250 | 37% helix, 25% strand | A0A1V2APZ1 |
| B, C | Beta-lactamase (EC 3.5.2.6) | protein | 246 | 38% helix, 25% strand | A0A1V2APZ1 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 244 | 38% helix, 25% strand | A0A1V2APZ1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.62 | 0.76 | 45 | empty |
| 2 | 288 | 0.54 | 0.76 | 40 | empty |
| 3 | 265 | 0.53 | 0.75 | 42 | empty |
| 4 | 246 | 0.50 | 0.75 | 37 | empty |
| 5 | 235 | 0.48 | 0.74 | 33 | empty |
Interfaces
4 interfaces between chains.
- B–D · 367 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 322 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 310 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 186 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 modified (carboxylation, engineered).
Compared structures
- 6V6N · The crystal structure of a class D beta-lactamase from Agrobacterium tumefaciens · 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 A0A1V2APZ1
- Elsewhere: RCSB PDB 6V6N · PDBe 6V6N · UniProt A0A1V2APZ1
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