Research workbench
Class a beta-lactamase sed-G238C complexed with imipenem
Analyse Class a beta-lactamase sed-G238C complexed with imipenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BFC
- Type
- protein
- Length
- 1,048 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
- Ligands
- IM2
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 42% 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 | 262 | 42% helix, 19% strand | Q93PQ0 |
Ligands and binding sites
- IM2 · (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.76 | 0.78 | 114 | empty |
| 2 | 344 | 0.71 | 0.84 | 57 | empty |
| 3 | 448 | 0.65 | 0.78 | 47 | IM2 |
| 4 | 126 | 0.44 | 0.77 | 21 | IM2 |
| 5 | 135 | 0.41 | 0.75 | 21 | IM2 |
Interfaces
4 interfaces between chains.
- C–D · 568 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 564 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 249 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 85 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 3BFC · class A beta-lactamase SED-G238C complexed with imipenem · 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 3BFC · PDBe 3BFC · UniProt Q93PQ0
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