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Structure-based redesign of cofactor binding in putrescine oxidase: A394C-A396T-Q431G triple mutant

Analyse Structure-based redesign of cofactor binding in putrescine oxidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2YG7
Type: protein
Length: 900 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putrescine oxidase
EC: 1.4.3.10
UniProt: B0F9F6
Ligands: FAD
Pockets: 5 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putrescine oxidase (EC 1.4.3.10)	protein	450	40% helix, 24% strand	B0F9F6

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	346	0.87	0.96	61	FAD
2	335	0.86	0.96	65	FAD
3	791	0.72	0.78	74	empty
4	67	0.50	0.85	26	empty
5	74	0.47	0.82	26	empty

Interfaces

1 interface between chains.

A–B · 236 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2YG7 · Structure-based redesign of cofactor binding in Putrescine Oxidase: A394C-A396T-Q431G… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt B0F9F6
Elsewhere: RCSB PDB 2YG7 · PDBe 2YG7 · UniProt B0F9F6

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