MolNFT v1 · #184764 · protein
Structure of kdnase from aspergillus terrerus in complex with 2-keto- 3-deoxynononic acid
7P1O · Sialidase domain-containing protein: “Structure of kdnase from aspergillus terrerus in complex with 2-keto- 3-deoxynononic acid”. X-ray diffraction, 3 ligands (SNN, KDM, CL), 7 pockets (best druggability 0.64). MolNFT v1 #184764 on…
- PDB
- 7P1O
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase domain-containing protein
- UniProt
- Q0CMX0
- Ligands
- SNN, KDM, CL
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, A | Sialidase domain-containing protein | protein | 385 | 5% helix, 44% strand | Q0CMX0 |
Ligands and binding sites
- SNN · L-3-aminosuccinimide · ligand · 2 copies · chains X, A
- KDM · deamino-alpha-neuraminic acid · ligand · 2 copies · chains X, A
- CL · Chloride ion · ion · chains X, A
- GOL · Glycerol · additive · chains X, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.64 | 0.81 | 31 | GOL, CL |
| 2 | 294 | 0.63 | 0.80 | 26 | empty |
| 3 | 378 | 0.62 | 0.78 | 54 | KDM |
| 4 | 269 | 0.62 | 0.80 | 28 | empty |
| 5 | 250 | 0.56 | 0.78 | 45 | KDM |
Interfaces
1 interface between chains.
- X–A · 562 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7P1O · Structure of KDNase from Aspergillus Terrerus in complex with 2-keto-3-deoxynononic acid · the same entry in another collection · chain X against X, 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 Q0CMX0
- Elsewhere: RCSB PDB 7P1O · PDBe 7P1O · UniProt Q0CMX0
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