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Crystal Structure of the Apo form of CMP-N-acetylneuraminate Synthetase from Vibrio cholerae
Analyse Crystal Structure of the Apo form of CMP-N-acetylneuraminate Synthetase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IFI
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Vibrio cholerae
- Molecule
- CMP-N-acetylneuraminate Synthetase
- EC
- 2.7.7.43
- Ligands
- CA
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · resolution 2.8 · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CMP-N-acetylneuraminate Synthetase (EC 2.7.7.43) | protein | 210 | 34% helix, 26% strand | — |
| B | CMP-N-acetylneuraminate Synthetase (EC 2.7.7.43) | protein | 218 | 33% helix, 25% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · 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 | 384 | 0.57 | 0.74 | 46 | empty |
| 2 | 272 | 0.52 | 0.75 | 33 | empty |
| 3 | 144 | 0.48 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1493 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6IFI · Crystal structure of the apo form of cmp-N-acetylneuraminate synthetase from vibrio… · 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
- Elsewhere: RCSB PDB 6IFI · PDBe 6IFI
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