Research workbench
Crystal structure of capsular polysaccharide synthesizing enzyme cape from staphylococcus aureus in complex with inihibitor
Analyse Crystal structure of capsular polysaccharide synthesizing enzyme cape from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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