MolNFT v1 · #145325 · protein
N. meningitidis cmp-sialic acid synthetase in the presence of cmp and NEU5AC2EN
6CKL · N-acylneuraminate cytidylyltransferase: “N. meningitidis cmp-sialic acid synthetase in the presence of cmp and NEU5AC2EN”. X-ray diffraction, 3 ligands (C5P, DAN, CL), 5 pockets (best druggability 0.88). MolNFT v1 #145325 on…
- PDB
- 6CKL
- Type
- protein
- Length
- 675 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylneuraminate cytidylyltransferase
- EC
- 2.7.7.43
- UniProt
- P0A0Z8
- Ligands
- C5P, DAN, CL
- Pockets
- 5 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | N-acylneuraminate cytidylyltransferase (EC 2.7.7.43) | protein | 225 | 32% helix, 25% strand | P0A0Z8 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 3 copies · chains A, B, C
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- FLC · Citrate anion · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.88 | 0.89 | 116 | DAN, FLC, C5P, CL |
| 2 | 430 | 0.80 | 0.88 | 44 | C5P, CL, DAN |
| 3 | 198 | 0.49 | 0.76 | 30 | C5P, CL |
| 4 | 110 | 0.37 | 0.75 | 17 | empty |
| 5 | 59 | 0.30 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1836 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 502 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 470 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6CKL · N. meningitidis CMP-sialic acid synthetase in the presence of CMP and Neu5Ac2en · 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 0.94
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 6CKL · PDBe 6CKL · UniProt P0A0Z8
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