Research workbench
Nadase from aspergillus fumigatus complexed with a substrate anologue
Analyse Nadase from aspergillus fumigatus complexed with a substrate anologue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YGG
- Type
- protein
- Length
- 418 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Afnadase
- UniProt
- Q4WL81
- Ligands
- DQV, NAG, FUC, CA, NA
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Afnadase | protein | 209 | 23% helix, 22% strand | Q4WL81 |
| B | Afnadase | protein | 209 | 23% helix, 22% strand | Q4WL81 |
Ligands and binding sites
- DQV · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.59 | 0.83 | 26 | empty |
| 2 | 157 | 0.57 | 0.82 | 26 | DQV |
| 3 | 194 | 0.54 | 0.78 | 24 | empty |
| 4 | 169 | 0.52 | 0.78 | 26 | empty |
| 5 | 100 | 0.48 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2321 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6YGG · NADase from Aspergillus fumigatus complexed with a substrate anologue · the same entry in another collection · chain B against B, 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 Q4WL81
- Elsewhere: RCSB PDB 6YGG · PDBe 6YGG · UniProt Q4WL81
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