Research workbench
Structural and biochemical evidence that a tem-1 {beta}-lactamase ASN170GLY active site mutant acts via substrate-assisted catalysis
Analyse Structural and biochemical evidence that a tem-1 {beta}-lactamase ASN170GLY… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JYI
- Type
- protein
- Length
- 1,578 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase tem
- EC
- 3.5.2.6
- UniProt
- P62593
- Ligands
- PO4
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Beta-lactamase tem (EC 3.5.2.6) | protein | 263 | 44% helix, 17% strand | P62593 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.64 | 0.74 | 57 | empty |
| 2 | 126 | 0.43 | 0.77 | 23 | EPE |
| 3 | 117 | 0.43 | 0.78 | 22 | EPE |
| 4 | 112 | 0.42 | 0.77 | 22 | EPE |
| 5 | 112 | 0.42 | 0.77 | 22 | EPE |
Interfaces
5 interfaces between chains.
- B–F · 441 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 436 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 210 Ų buried · 2 hydrogen bonds · protein-protein
- C–E · 24 Ų buried · 0 hydrogen bonds · protein-protein
- D–F · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3JYI · Structural and biochemical evidence that a TEM-1 {beta}-lactamase Asn170Gly active site… · the same entry in another collection · chain F against F, TM-score 1.00
- P62593 · AlphaFold monomer V2.0 prediction for beta-lactamase tem (P62593) · a predicted model of the same protein · chain E 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 3JYI · PDBe 3JYI · UniProt P62593
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