Research workbench
The crystal structure of murine cmp-5-N-acetylneuraminic acid synthetase
Analyse The crystal structure of murine cmp-5-N-acetylneuraminic acid synthetase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QWJ
- Type
- protein
- Length
- 913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytidine monophospho-N-acetylneuraminic acid synthetase
- EC
- 2.7.7.43
- UniProt
- Q99KK2
- Ligands
- NCC
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Cytidine monophospho-N-acetylneuraminic acid synthetase (EC 2.7.7.43) | protein | 228 | 30% helix, 24% strand | Q99KK2 |
| B | Cytidine monophospho-N-acetylneuraminic acid synthetase (EC 2.7.7.43) | protein | 229 | 31% helix, 24% strand | Q99KK2 |
Ligands and binding sites
- NCC · Cytidine-5'-monophosphate-5-N-acetylneuraminic acid · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.86 | 0.87 | 108 | NCC |
| 2 | 702 | 0.84 | 0.88 | 77 | NCC |
| 3 | 217 | 0.68 | 0.86 | 27 | NCC |
| 4 | 319 | 0.63 | 0.79 | 32 | empty |
| 5 | 344 | 0.60 | 0.77 | 38 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2330 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 2067 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 460 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1QWJ · The Crystal Structure of Murine CMP-5-N-Acetylneuraminic Acid Synthetase · the same entry in another collection · chain A against A, TM-score 1.00
- Q99KK2 · AlphaFold monomer V2.0 prediction for N-acylneuraminate cytidylyltransferase (Q99KK2) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q99KK2
- Elsewhere: RCSB PDB 1QWJ · PDBe 1QWJ · UniProt Q99KK2
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