MolNFT v1 · #38926 · protein
Ampc beta-lactamase in complex with 2-acetamidothiophene-3-carboxylic acid
2HDU: “Ampc beta-lactamase in complex with 2-acetamidothiophene-3-carboxylic acid”. X-ray diffraction, 3 ligands (F12, K, PO4), 10 pockets (best druggability 0.82). MolNFT v1 #38926 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2HDU
- Type
- protein
- Length
- 716 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
- F12, K, PO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 39% helix, 23% strand | P00811 |
Ligands and binding sites
- F12 · 2-(acetylamino)thiophene-3-carboxylic acid · ligand · 8 copies · chains A, B
- K · Potassium ion · metal · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.82 | 0.98 | 29 | F12 |
| 2 | 454 | 0.68 | 0.80 | 59 | F12 |
| 3 | 341 | 0.66 | 0.81 | 56 | F12 |
| 4 | 297 | 0.63 | 0.80 | 62 | K |
| 5 | 141 | 0.59 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 857 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2HDU · AmpC beta-lactamase in complex with 2-acetamidothiophene-3-carboxylic acid · 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 2HDU · PDBe 2HDU · UniProt P00811
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.