Research workbench
Ampc beta-lactamase in complex with 5-diformylaminomethyl- BENZO[B]THIOPHEN-2-boronic acid
Analyse Ampc beta-lactamase in complex with 5-diformylaminomethyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I72
- Type
- protein
- Length
- 705 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P00811
- Ligands
- VA1
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 40% helix, 23% strand | P00811 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 347 | 38% helix, 24% strand | P00811 |
Ligands and binding sites
- VA1 · {5-[(diformylamino)methyl]-1-benzothien-2-yl}boronic acid · ligand · 2 copies · chains A, B
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 | 435 | 0.78 | 0.86 | 71 | empty |
| 2 | 312 | 0.64 | 0.81 | 49 | VA1 |
| 3 | 328 | 0.55 | 0.75 | 50 | VA1 |
| 4 | 109 | 0.48 | 0.81 | 31 | empty |
| 5 | 71 | 0.32 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 742 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2I72 · AmpC beta-lactamase in complex with 5-diformylaminomethyl-benzo[b]thiophen-2-boronic acid · the same entry in another collection · chain A against A, TM-score 1.00
- 1L2S · X-ray crystal structure of ampc beta-lactamase from E. COLI in complex with a… · a predicted model of the same protein · chain A against B, TM-score 1.00
- 1L2S · X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with a… · a predicted model of the same protein · chain A against B, TM-score 1.00
- P00811 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00811) · a predicted model of the same protein · 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 P00811
- Elsewhere: RCSB PDB 2I72 · PDBe 2I72 · UniProt P00811
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