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Structure of kdnase from trichophyton rubrum in complex with 2-keto-3- deoxynononic acid

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

PDB: 7P1Q
Type: protein
Length: 383 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Extracellular SIALIDASE/NEURAMINIDASE
UniProt: A0A178EUH2
Ligands: KDM
Pockets: 3 · best druggability 0.62

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Extracellular SIALIDASE/NEURAMINIDASE	protein	383	5% helix, 44% strand	A0A178EUH2

Ligands and binding sites

KDM · deamino-alpha-neuraminic acid · ligand · 3 copies · chains A
GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	335	0.62	0.79	31	empty
2	206	0.54	0.78	41	KDM
3	50	0.30	0.77	18	empty

Compared structures

7P1Q · Structure of KDNase from Trichophyton Rubrum 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 A0A178EUH2
Elsewhere: RCSB PDB 7P1Q · PDBe 7P1Q · UniProt A0A178EUH2

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