MolNFT v1 · #152366 · protein
Crystal structure of cmp-N-acetylneuraminate synthetase from vibrio cholerae in complex with cdp and MG2+.
6IFD: “Crystal structure of cmp-N-acetylneuraminate synthetase from vibrio cholerae in complex with cdp and MG2+.”. X-ray diffraction, 3 ligands (CDP, CA, MG), 11 pockets (best druggability 0.79). MolNFT v1 #152366 on GenesisL1: 3D…
- PDB
- 6IFD
- Type
- protein
- Length
- 896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cmp-N-acetylneuraminate synthetase
- EC
- 2.7.7.43
- Ligands
- CDP, CA, MG
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cmp-N-acetylneuraminate synthetase (EC 2.7.7.43) | protein | 217 | 35% helix, 26% strand | — |
| B | Cmp-N-acetylneuraminate synthetase (EC 2.7.7.43) | protein | 234 | 39% helix, 24% strand | — |
| C | Cmp-N-acetylneuraminate synthetase (EC 2.7.7.43) | protein | 227 | 36% helix, 25% strand | — |
| D | Cmp-N-acetylneuraminate synthetase (EC 2.7.7.43) | protein | 218 | 36% helix, 25% strand | — |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · chains B
- MG · Magnesium ion · metal · chains C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, D
- PGE · Triethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.79 | 0.84 | 43 | CDP, MG, PG4 |
| 2 | 471 | 0.76 | 0.85 | 44 | CDP, PGE |
| 3 | 384 | 0.73 | 0.84 | 41 | empty |
| 4 | 500 | 0.71 | 0.81 | 45 | empty |
| 5 | 422 | 0.61 | 0.76 | 58 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1775 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1438 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 404 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 271 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 261 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6IFD · Crystal Structure of CMP-N-acetylneuraminate Synthetase from Vibrio cholerae in complex… · 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
- Elsewhere: RCSB PDB 6IFD · PDBe 6IFD
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