Research workbench

Structure of kdnase from aspergillus terrerus in complex with 2-keto- 3-deoxynononic acid

Analyse Structure of kdnase from aspergillus terrerus in complex with 2-keto… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7P1D
Type: protein
Length: 383 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sialidase domain-containing protein
UniProt: Q0CMX0
Ligands: KDM, SNN, CA
Pockets: 2 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sialidase domain-containing protein	protein	383	5% helix, 44% strand	Q0CMX0

Ligands and binding sites

KDM · deamino-alpha-neuraminic acid · ligand · 2 copies · chains A
SNN · L-3-aminosuccinimide · ligand · chains A
CA · Calcium 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	296	0.64	0.80	25	empty
2	279	0.57	0.77	42	KDM

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

7P1D · Structure of KDNase from Aspergillus Terrerus in complex with 2-keto-3-deoxynononic acid · 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 7P1D · PDBe 7P1D · UniProt Q0CMX0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.