MolNFT v1 · #95312 · protein
Crystal structure of pasteurella multocida N-acetyl-D-neuraminic acid lyase K164 mutant complexed with N-acetylneuraminic acid
4IMF · N-acetylneuraminate lyase: “Crystal structure of pasteurella multocida N-acetyl-D-neuraminic acid lyase K164 mutant complexed with…”. X-ray diffraction, 3 ligands (ME2, SI3, CL), 4 pockets (best druggability 0.71). MolNFT v1 #95312…
- PDB
- 4IMF
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- Q9CKB0
- Ligands
- ME2, SI3, CL
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 292 | 53% helix, 14% strand | Q9CKB0 |
Ligands and binding sites
- ME2 · 1-ethoxy-2-(2-methoxyethoxy)ethane · ligand · 3 copies · chains A, B
- SI3 · 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.71 | 0.88 | 32 | empty |
| 2 | 292 | 0.69 | 0.83 | 41 | SI3 |
| 3 | 287 | 0.67 | 0.82 | 41 | SI3 |
| 4 | 71 | 0.35 | 0.77 | 25 | ME2 |
Interfaces
1 interface between chains.
- A–B · 1430 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4IMF · Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic acid lyase K164 mutant… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9CKB0 · AlphaFold monomer V2.0 prediction for N-acetylneuraminate lyase (Q9CKB0) · 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 Q9CKB0
- Elsewhere: RCSB PDB 4IMF · PDBe 4IMF · UniProt Q9CKB0
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