MolNFT v1 · #188670 · protein
Ampicillin-ctx-M-15
7U4B · Beta-lactamase: “Ampicillin-ctx-M-15”. X-ray diffraction, 2 ligands (NW3, SO4), 7 pockets (best druggability 0.54). MolNFT v1 #188670 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7U4B
- Type
- protein
- Length
- 780 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- C7S9T0
- Ligands
- NW3, SO4
- Pockets
- 7 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Beta-lactamase (EC 3.5.2.6) | protein | 260 | 43% helix, 19% strand | C7S9T0 |
Ligands and binding sites
- NW3 · (2S,4S)-2-[(1S)-1-{[(2S)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.54 | 0.75 | 57 | NW3 |
| 2 | 178 | 0.53 | 0.79 | 24 | empty |
| 3 | 110 | 0.50 | 0.81 | 22 | empty |
| 4 | 227 | 0.49 | 0.75 | 30 | empty |
| 5 | 156 | 0.45 | 0.75 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 767 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 333 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7U4B · Ampicillin-CTX-M-15 · 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 C7S9T0
- Elsewhere: RCSB PDB 7U4B · PDBe 7U4B · UniProt C7S9T0
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