Research workbench
Vanin-1 complexed with compound 3
Analyse Vanin-1 complexed with compound 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SLV
- Type
- protein
- Length
- 461 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pantetheinase
- EC
- 3.5.1.92
- UniProt
- O95497
- Ligands
- 9TC, BMA, NAG, NA
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pantetheinase (EC 3.5.1.92) | protein | 461 | 18% helix, 36% strand | O95497 |
Ligands and binding sites
- 9TC · (8-oxa-2-azaspiro[4.5]decan-2-yl)(2-{[(pyrazin-2-yl) methyl]amino}pyrimidin-5-yl)methanone · ligand · chains A
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.68 | 0.86 | 26 | 9TC |
| 2 | 173 | 0.53 | 0.79 | 26 | empty |
Modifications
Observed in the structure: 5 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 O95497
- Elsewhere: RCSB PDB 7SLV · PDBe 7SLV · UniProt O95497
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