MolNFT v1 · #68726 · protein

Aspergillus niger phytase

3K4P · 3-phytase a: “Aspergillus niger phytase”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.52). MolNFT v1 #68726 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3K4P
Type: protein
Length: 876 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-phytase a
EC: 3.1.3.8
UniProt: P34752
Ligands: NAG
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	3-phytase a (EC 3.1.3.8)	protein	438	44% helix, 12% strand	P34752

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	301	0.52	0.75	39	empty
2	202	0.50	0.76	27	empty
3	260	0.50	0.75	32	empty
4	165	0.48	0.76	24	empty

Modifications

Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

3K4P · Aspergillus niger Phytase · the same entry in another collection · chain A against A, TM-score 1.00
P34752 · AlphaFold monomer V2.0 prediction for 3-phytase a (P34752) · a predicted model of the same protein · 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 P34752
Elsewhere: RCSB PDB 3K4P · PDBe 3K4P · UniProt P34752

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