MolNFT v1 · #95310 · protein
Crystal structure of pasteurella multocida N-acetyl-D-neuraminic acid lyase trapped with pyruvate covalently bound through a schiff base to LYS164
4IMD · N-acetylneuraminate lyase: “Crystal structure of pasteurella multocida N-acetyl-D-neuraminic acid lyase trapped with pyruvate covalently…”. X-ray diffraction, 1 ligand (PO4), 9 pockets (best druggability 0.73). MolNFT v1 #95310 on…
- PDB
- 4IMD
- Type
- protein
- Length
- 1,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- Q9CKB0
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 292 | 52% helix, 14% strand | Q9CKB0 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.73 | 0.89 | 29 | empty |
| 2 | 185 | 0.72 | 0.89 | 31 | empty |
| 3 | 347 | 0.66 | 0.80 | 39 | EDO |
| 4 | 356 | 0.66 | 0.80 | 42 | EDO |
| 5 | 343 | 0.65 | 0.80 | 43 | EDO |
Interfaces
4 interfaces between chains.
- B–C · 1456 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1440 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1110 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1109 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 4IMD · Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic acid lyase trapped with… · the same entry in another collection · chain B against B, 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 4IMD · PDBe 4IMD · UniProt Q9CKB0
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