MolNFT v1 · #13073 · protein
X-ray crystal structure of ampc S64D mutant beta-lactamase
1L0D: “X-ray crystal structure of ampc S64D mutant beta-lactamase”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.78). MolNFT v1 #13073 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1L0D
- Type
- protein
- Length
- 709 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
- PO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 351 | 38% helix, 24% strand | P00811 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 358 | 41% helix, 23% strand | P00811 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
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 | 567 | 0.78 | 0.84 | 69 | empty |
| 2 | 319 | 0.67 | 0.82 | 57 | empty |
| 3 | 471 | 0.62 | 0.76 | 48 | empty |
| 4 | 126 | 0.49 | 0.79 | 32 | empty |
| 5 | 70 | 0.31 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 679 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1L0D · X-ray Crystal Structure of AmpC S64D Mutant beta-Lactamase · 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
- 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 1L0D · PDBe 1L0D · UniProt P00811
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