Research workbench
Crystal structure of the class a beta-lactamase sed-G238C mutant from citrobacter sedlakii
Analyse Crystal structure of the class a beta-lactamase sed-G238C mutant from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BFD
- Type
- protein
- Length
- 1,052 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class a beta-lactamase SED1
- EC
- 3.5.2.6
- UniProt
- Q93PQ0
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Class a beta-lactamase SED1 (EC 3.5.2.6) | protein | 263 | 43% helix, 19% strand | Q93PQ0 |
Ligands and binding sites
- CAC · Cacodylate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.78 | 0.80 | 112 | empty |
| 2 | 360 | 0.73 | 0.85 | 58 | empty |
| 3 | 482 | 0.66 | 0.78 | 49 | CAC |
| 4 | 126 | 0.45 | 0.77 | 21 | CAC |
| 5 | 113 | 0.43 | 0.78 | 22 | CAC |
Interfaces
4 interfaces between chains.
- A–B · 570 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 567 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 329 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 156 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3BFD · Crystal Structure of the Class A beta-lactamase SED-G238C mutant from Citrobacter sedlakii · 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 Q93PQ0
- Elsewhere: RCSB PDB 3BFD · PDBe 3BFD · UniProt Q93PQ0
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