MolNFT v1 · #82921 · protein
Crystal structure of capsular polysaccharide synthesizing enzyme cape from staphylococcus aureus in complex with inihibitor
3W1V · Capsular polysaccharide synthesis enzyme CAP8E: “Crystal structure of capsular polysaccharide synthesizing enzyme cape from staphylococcus aureus in complex…”. X-ray diffraction, 3 ligands (UDZ, NA, SO4), 5 pockets (best…
- PDB
- 3W1V
- Type
- protein
- Length
- 693 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsular polysaccharide synthesis enzyme CAP8E
- EC
- 4.2.1.115
- UniProt
- Q7A2Y4
- Ligands
- UDZ, NA, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsular polysaccharide synthesis enzyme CAP8E (EC 4.2.1.115) | protein | 347 | 42% helix, 19% strand | Q7A2Y4 |
| B | Capsular polysaccharide synthesis enzyme CAP8E (EC 4.2.1.115) | protein | 346 | 41% helix, 18% strand | Q7A2Y4 |
Ligands and binding sites
- UDZ · [(2R,3S,4R,5R,6R)-5-acetamido-6-[[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,4-bis(oxidanyl)oxan-2-yl]methylimino-azanylidene-azanium · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 14 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 769 | 0.80 | 0.83 | 73 | UDZ |
| 2 | 813 | 0.79 | 0.82 | 81 | SO4, UDZ |
| 3 | 119 | 0.77 | 0.96 | 27 | empty |
| 4 | 462 | 0.72 | 0.82 | 58 | EPE |
| 5 | 50 | 0.26 | 0.73 | 11 | SO4 |
Interfaces
1 interface between chains.
- A–B · 2571 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3W1V · Crystal Structure of Capsular Polysaccharide Synthesizing Enzyme CapE from Staphylococcus… · 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 Q7A2Y4
- Elsewhere: RCSB PDB 3W1V · PDBe 3W1V · UniProt Q7A2Y4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.