Research workbench
Crystal structure of N-acetylneuraminate lyase from E. COLI mutant L142R in complex with B-hydroxypyruvate
Analyse Crystal structure of N-acetylneuraminate lyase from E. COLI mutant L142R in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HL2
- Type
- protein
- Length
- 1,178 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylneuraminate lyase subunit
- EC
- 4.1.3.3
- UniProt
- P06995
- Ligands
- 3PY
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | N-acetylneuraminate lyase subunit (EC 4.1.3.3) | protein | 295 | 54% helix, 13% strand | P06995 |
| B | N-acetylneuraminate lyase subunit (EC 4.1.3.3) | protein | 293 | 54% helix, 13% strand | P06995 |
Ligands and binding sites
- 3PY · 3-hydroxypyruvic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.78 | 0.93 | 26 | empty |
| 2 | 178 | 0.76 | 0.92 | 24 | empty |
| 3 | 306 | 0.71 | 0.85 | 32 | empty |
| 4 | 306 | 0.70 | 0.84 | 31 | empty |
| 5 | 324 | 0.70 | 0.83 | 32 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1283 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1268 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1046 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1034 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1HL2 · Crystal structure of N-acetylneuraminate lyase from E. coli mutant L142R in complex with… · 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 P06995
- Elsewhere: RCSB PDB 1HL2 · PDBe 1HL2 · UniProt P06995
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.