Research workbench
Crystal structure of a novel N-acetylneuraminic acid lyase from Corynebacterium glutamicum
Analyse Crystal structure of a novel N-acetylneuraminic acid lyase from Corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C54
- Type
- protein
- Length
- 2,473 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.601
- Source
- Corynebacterium glutamicum ATCC 13032
- Molecule
- Dihydrodipicolinate synthase/N-acetylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- Q8NMD2
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.601 · 4 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, H | Dihydrodipicolinate synthase/N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 310 | 50% helix, 10% strand | Q8NMD2 |
| D | Dihydrodipicolinate synthase/N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 308 | 50% helix, 10% strand | Q8NMD2 |
| E | Dihydrodipicolinate synthase/N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 308 | 50% helix, 10% strand | Q8NMD2 |
| G | Dihydrodipicolinate synthase/N-acetylneuraminate lyase (EC 4.1.3.3) | protein | 307 | 51% helix, 10% strand | Q8NMD2 |
Ligands and binding sites
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.71 | 0.80 | 63 | GOL |
| 2 | 500 | 0.70 | 0.80 | 54 | GOL |
| 3 | 484 | 0.70 | 0.80 | 55 | GOL |
| 4 | 475 | 0.70 | 0.80 | 54 | GOL |
| 5 | 471 | 0.70 | 0.80 | 55 | GOL |
Interfaces
10 interfaces between chains.
- C–D · 1972 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1965 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1965 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 1956 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 931 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5C54 · Crystal structure of a novel N-acetylneuraminic acid lyase from corynebacterium glutamicum · 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 5C54 · PDBe 5C54 · UniProt Q8NMD2
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