MolNFT v1 · #157855 · protein
Crystal structure of N-acetylneuraminic acid (sialic acid) synthetase from leptospira borgpetersenii serovar hardjo-bovis in complex with citrate
6NCS: “Crystal structure of N-acetylneuraminic acid (sialic acid) synthetase from leptospira borgpetersenii serovar…”. X-ray diffraction, 2 ligands (MN, IOD), 8 pockets (best druggability 0.68). MolNFT v1 #157855 on GenesisL1: 3D…
- PDB
- 6NCS
- Type
- protein
- Length
- 570 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylneuraminic acid (sialic acid) synthetase
- UniProt
- Q04TM5
- Ligands
- MN, IOD
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetylneuraminic acid (sialic acid) synthetase | protein | 285 | 46% helix, 18% strand | Q04TM5 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 20 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
- FMT · Formic acid · additive · chains A, B
- TAR · D(-)-tartaric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.68 | 0.84 | 30 | MN, CIT |
| 2 | 254 | 0.66 | 0.82 | 28 | MN, CIT |
| 3 | 100 | 0.55 | 0.85 | 23 | empty |
| 4 | 104 | 0.49 | 0.82 | 25 | empty |
| 5 | 103 | 0.48 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3061 Ų buried · 79 hydrogen bonds · protein-protein
Compared structures
- 6NCS · Crystal structure of N-acetylneuraminic acid (Sialic acid) synthetase from Leptospira… · 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
- Every structure of UniProt Q04TM5
- Elsewhere: RCSB PDB 6NCS · PDBe 6NCS · UniProt Q04TM5
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