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Structure of a sialic acid activating synthetase, cmp acylneuraminate synthetase in the presence and absence of cdp
Analyse Structure of a sialic acid activating synthetase, cmp acylneuraminate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EYR
- Type
- protein
- Length
- 446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cmp-N-acetylneuraminic acid synthetase
- EC
- 2.7.7.43
- UniProt
- P0A0Z8
- Ligands
- CDP
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cmp-N-acetylneuraminic acid synthetase (EC 2.7.7.43) | protein | 225 | 32% helix, 24% strand | P0A0Z8 |
| B | Cmp-N-acetylneuraminic acid synthetase (EC 2.7.7.43) | protein | 221 | 33% helix, 24% strand | P0A0Z8 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.67 | 0.77 | 57 | CDP |
| 2 | 529 | 0.64 | 0.76 | 44 | CDP |
Interfaces
1 interface between chains.
- A–B · 1393 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 1EYR · Structure of a sialic acid activating synthetase, CMP acylneuraminate synthetase in the… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A0Z8 · AlphaFold monomer V2.0 prediction for N-acylneuraminate cytidylyltransferase (P0A0Z8) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P0A0Z8
- Elsewhere: RCSB PDB 1EYR · PDBe 1EYR · UniProt P0A0Z8
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