MolNFT v1 · #145324 · protein
N. meningitidis cmp-sialic acid synthetase in the presence of CTP and CA2+
6CKK · N-acylneuraminate cytidylyltransferase: “N. meningitidis cmp-sialic acid synthetase in the presence of CTP and CA2+”. X-ray diffraction, 2 ligands (CTP, CA), 3 pockets (best druggability 0.71). MolNFT v1 #145324 on GenesisL1: 3D…
- PDB
- 6CKK
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylneuraminate cytidylyltransferase
- EC
- 2.7.7.43
- UniProt
- P0A0Z8
- Ligands
- CTP, CA
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acylneuraminate cytidylyltransferase (EC 2.7.7.43) | protein | 225 | 33% helix, 24% strand | P0A0Z8 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 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 | 619 | 0.71 | 0.79 | 44 | CTP |
| 2 | 513 | 0.62 | 0.75 | 45 | CTP, CA |
| 3 | 65 | 0.37 | 0.78 | 17 | CA |
Interfaces
1 interface between chains.
- A–B · 1466 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6CKK · N. meningitidis CMP-sialic acid synthetase in the presence of CTP and Ca2+ · 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 A against A, TM-score 0.95
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 6CKK · PDBe 6CKK · UniProt P0A0Z8
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