Research workbench
Crystal structure of ampc beta-lactamase in complex with covalently bound N-formyl 7-aminocephalosporanic acid
Analyse Crystal structure of ampc beta-lactamase in complex with covalently bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OLG
- Type
- protein
- Length
- 714 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
- 2TV, PO4
- Pockets
- 9 · best druggability 0.80
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 | 356 | 39% helix, 23% strand | P00811 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 40% helix, 23% strand | P00811 |
Ligands and binding sites
- 2TV · (2R,5Z)-5-[(acetyloxy)methylidene]-2-[(1R)-1-(formylamino)-2-oxoethyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
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 | 442 | 0.80 | 0.87 | 60 | empty |
| 2 | 544 | 0.67 | 0.78 | 56 | 2TV |
| 3 | 320 | 0.67 | 0.82 | 51 | 2TV |
| 4 | 74 | 0.45 | 0.81 | 22 | empty |
| 5 | 65 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 683 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4OLG · Crystal structure of AmpC beta-lactamase in complex with covalently bound N-formyl… · the same entry in another collection · chain B 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 B 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 B against B, TM-score 1.00
- P00811 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00811) · a predicted model of the same protein · chain B 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 4OLG · PDBe 4OLG · UniProt P00811
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