MolNFT v1 · #184756 · protein
Structure of kdnase from aspergillus terrerus in complex with 2,3- didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid.
7P1F · Sialidase domain-containing protein: “Structure of kdnase from aspergillus terrerus in complex with 2,3…”. X-ray diffraction, 3 ligands (SNN, KFN, CA), 6 pockets (best druggability 0.66). MolNFT v1 #184756 on GenesisL1: 3D…
- PDB
- 7P1F
- Type
- protein
- Length
- 767 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase domain-containing protein
- UniProt
- Q0CMX0
- Ligands
- SNN, KFN, CA
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Sialidase domain-containing protein | protein | 383 | 5% helix, 44% strand | Q0CMX0 |
| A | Sialidase domain-containing protein | protein | 384 | 5% helix, 44% strand | Q0CMX0 |
Ligands and binding sites
- SNN · L-3-aminosuccinimide · ligand · 2 copies · chains B, A
- KFN · 2,6-anhydro-3-deoxy-D-glycero-D-galacto-non-2-enonic acid · ligand · 2 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains B, A
- GOL · Glycerol · additive · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.66 | 0.81 | 32 | empty |
| 2 | 300 | 0.63 | 0.80 | 27 | empty |
| 3 | 398 | 0.62 | 0.77 | 65 | KFN |
| 4 | 269 | 0.62 | 0.80 | 26 | empty |
| 5 | 283 | 0.57 | 0.78 | 48 | KFN |
Interfaces
1 interface between chains.
- B–A · 538 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7P1F · Structure of KDNase from Aspergillus terrerus in complex with… · 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 Q0CMX0
- Elsewhere: RCSB PDB 7P1F · PDBe 7P1F · UniProt Q0CMX0
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