MolNFT v1 · #38925 · protein
Ampc beta-lactamase in complex with 4-methanesulfonylamino benzoic acid
2HDS: “Ampc beta-lactamase in complex with 4-methanesulfonylamino benzoic acid”. X-ray diffraction, 5 ligands (4MB, GLC, FRU), 8 pockets (best druggability 0.78). MolNFT v1 #38925 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2HDS
- 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
- 4MB, GLC, FRU, NA, PO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 39% helix, 24% strand | P00811 |
Ligands and binding sites
- 4MB · 4-[(methylsulfonyl)amino]benzoic acid · ligand · 3 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- NA · Sodium ion · metal · chains B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.78 | 0.82 | 82 | empty |
| 2 | 289 | 0.66 | 0.82 | 53 | empty |
| 3 | 337 | 0.62 | 0.79 | 47 | FRU, PO4, 4MB |
| 4 | 103 | 0.45 | 0.78 | 25 | 4MB |
| 5 | 73 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 659 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2HDS · AmpC beta-lactamase in complex with 4-Methanesulfonylamino benzoic acid · the same entry in another collection · 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
- 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
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 2HDS · PDBe 2HDS · UniProt P00811
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