Research workbench
Crystal structure of the Y138F mutant of C.GLUTAMICUM N- acetylneuraminic acid lyase in complex with pyruvate
Analyse Crystal structure of the Y138F mutant of C.GLUTAMICUM N- acetylneuraminic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C55
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate SYNTHASE/N-acetylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- Q8NMD2
- Ligands
- PYR
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate SYNTHASE/N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 307 | 50% helix, 10% strand | Q8NMD2 |
| B | Dihydrodipicolinate SYNTHASE/N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 306 | 52% helix, 10% strand | Q8NMD2 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.69 | 0.83 | 42 | EDO, PYR, GOL |
| 2 | 293 | 0.69 | 0.83 | 45 | PYR, EDO |
| 3 | 51 | 0.47 | 0.86 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1958 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5C55 · Crystal structure of the Y138F mutant of C.glutamicum N-acetylneuraminic acid lyase in… · the same entry in another collection · 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 Q8NMD2
- Elsewhere: RCSB PDB 5C55 · PDBe 5C55 · UniProt Q8NMD2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.