Research workbench
Class a beta-lactamase sed-G238C complexed with faropenem
Analyse Class a beta-lactamase sed-G238C complexed with faropenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BFF
- 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
- SFR, FPM, SCN
- Pockets
- 9 · best druggability 0.78
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
- SFR · (2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- FPM · (5R,6S)-6-(1-hydroxyethyl)-7-oxo-3-[(2R)-oxolan-2-yl]-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid · ligand · chains C
- SCN · Thiocyanate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.78 | 0.80 | 89 | empty |
| 2 | 334 | 0.73 | 0.85 | 52 | empty |
| 3 | 438 | 0.66 | 0.79 | 48 | SFR |
| 4 | 155 | 0.44 | 0.75 | 28 | empty |
| 5 | 111 | 0.41 | 0.77 | 19 | SFR |
Interfaces
4 interfaces between chains.
- A–B · 563 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 557 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 322 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 97 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide (covalent ligand, disulfide).
Compared structures
- 3BFF · class A beta-lactamase SED-G238C complexed with faropenem · 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 3BFF · PDBe 3BFF · UniProt Q93PQ0
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