MolNFT v1 · #6258 · protein
Crystal structure analysis of N-acetylneuraminate lyase from haemophilus influenzae: crystal form III in complex with sialic acid alditol
1F73 · N-acetyl neuraminate lyase: “Crystal structure analysis of N-acetylneuraminate lyase from haemophilus influenzae: crystal form III in…”. X-ray diffraction, 1 ligand (HMN), 8 pockets (best druggability 0.70). MolNFT v1 #6258 on…
- PDB
- 1F73
- Type
- protein
- Length
- 1,152 residues
- Chains
- 4
- 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
- HMN
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | N-acetyl neuraminate lyase (EC 4.1.3.3) | protein | 288 | 54% helix, 14% strand | P44539 |
Ligands and binding sites
- HMN · 2,4,6,7,8,9-hexahydroxy-5-methylcarboxamido nonanoic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.70 | 0.88 | 28 | GOL |
| 2 | 201 | 0.70 | 0.87 | 34 | empty |
| 3 | 654 | 0.69 | 0.77 | 63 | HMN |
| 4 | 496 | 0.67 | 0.78 | 45 | HMN |
| 5 | 418 | 0.65 | 0.78 | 39 | HMN |
Interfaces
4 interfaces between chains.
- B–C · 1301 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1298 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1164 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1116 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1F73 · 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 1F73 · PDBe 1F73 · UniProt P44539
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