Research workbench
A triple mutant in the omega-loop of tem-1 beta-lactamase changes the substrate profile via a large conformational change and an altered general base for catalysis
Analyse A triple mutant in the omega-loop of tem-1 beta-lactamase changes the substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RX2
- Type
- protein
- Length
- 2,036 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase tem
- EC
- 3.5.2.6
- UniProt
- P62593
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase tem (EC 3.5.2.6) | protein | 255 | 47% helix, 19% strand | P62593 |
| B, D | Beta-lactamase tem (EC 3.5.2.6) | protein | 256 | 45% helix, 18% strand | P62593 |
| C | Beta-lactamase tem (EC 3.5.2.6) | protein | 258 | 44% helix, 19% strand | P62593 |
| E | Beta-lactamase tem (EC 3.5.2.6) | protein | 252 | 44% helix, 17% strand | P62593 |
| F | Beta-lactamase tem (EC 3.5.2.6) | protein | 254 | 45% helix, 18% strand | P62593 |
| G | Beta-lactamase tem (EC 3.5.2.6) | protein | 252 | 46% helix, 17% strand | P62593 |
| H | Beta-lactamase tem (EC 3.5.2.6) | protein | 253 | 44% helix, 18% strand | P62593 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.75 | 0.79 | 84 | empty |
| 2 | 887 | 0.69 | 0.75 | 94 | SO4 |
| 3 | 401 | 0.68 | 0.81 | 56 | empty |
| 4 | 474 | 0.67 | 0.78 | 56 | empty |
| 5 | 530 | 0.66 | 0.77 | 67 | SO4 |
Interfaces
15 interfaces between chains.
- F–H · 705 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 676 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 493 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 480 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4RX2 · A triple mutant in the omega-loop of TEM-1 beta-lactamase changes the substrate profile… · the same entry in another collection · chain G against G, TM-score 1.00
- P62593 · AlphaFold monomer V2.0 prediction for beta-lactamase tem (P62593) · a predicted model of the same protein · chain G 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 P62593
- Elsewhere: RCSB PDB 4RX2 · PDBe 4RX2 · UniProt P62593
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