Research workbench
Crystal structure of pasteurella multocida N-acetyl-D-neuraminic acid lyase K164A mutant
Analyse Crystal structure of pasteurella multocida N-acetyl-D-neuraminic acid lyase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IME
- Type
- protein
- Length
- 2,344 residues
- Chains
- 8
- 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
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 293 | 53% helix, 14% strand | Q9CKB0 |
Ligands and binding sites
- ME2 · 1-ethoxy-2-(2-methoxyethoxy)ethane · ligand · 7 copies · chains A, B, C, D, E, F, G, H
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.83 | 0.84 | 102 | empty |
| 2 | 685 | 0.70 | 0.78 | 64 | empty |
| 3 | 349 | 0.70 | 0.82 | 42 | empty |
| 4 | 387 | 0.70 | 0.81 | 42 | empty |
| 5 | 163 | 0.70 | 0.89 | 30 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1432 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1427 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1420 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1395 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1119 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4IME · Crystal Structure of Pasteurella multocida N-Acetyl-D-Neuraminic acid lyase K164A Mutant · the same entry in another collection · chain H against H, 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 4IME · PDBe 4IME · UniProt Q9CKB0
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