Research workbench
Crystal structure analysis of N-acetylneuraminate lyase from haemophilus influenzae: crystal form II in complex with 4-oxo-sialic acid
Analyse Crystal structure analysis of N-acetylneuraminate lyase from haemophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F7B
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyl-neuraminate lyase
- EC
- 4.1.3.3
- UniProt
- P44539
- Ligands
- NAU, NAV, CL
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyl-neuraminate lyase (EC 4.1.3.3) | protein | 293 | 54% helix, 14% strand | P44539 |
| C | N-acetyl-neuraminate lyase (EC 4.1.3.3) | protein | 285 | 53% helix, 14% strand | P44539 |
Ligands and binding sites
- NAU · 4,4,6,7,8,9-hexahydroxy-5-methylcarboxamidononanoic acid · ligand · chains A
- NAV · 6,7,8,9-tetrahydroxy-5-methylcarboxamido-4-oxononanoic acid · ligand · chains C
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.57 | 0.77 | 26 | NAU |
| 2 | 106 | 0.38 | 0.75 | 21 | NAV |
| 3 | 64 | 0.33 | 0.75 | 13 | empty |
| 4 | 57 | 0.27 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 1133 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1F7B · Crystal structure analysis of N-acetylneuraminate lyase from haemophilus influenzae… · the same entry in another collection · chain A against A, TM-score 1.00
- P44539 · AlphaFold monomer V2.0 prediction for N-acetylneuraminate lyase (P44539) · a predicted model of the same protein · 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 P44539
- Elsewhere: RCSB PDB 1F7B · PDBe 1F7B · UniProt P44539
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