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Yeast polyamine oxidase FMS1, N195A mutant

Analyse Yeast polyamine oxidase FMS1, N195A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GDP
Type: protein
Length: 1,982 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyamine oxidase FMS1
EC: 1.5.3.17
UniProt: P50264
Ligands: FAD
Pockets: 17 · best druggability 0.88

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polyamine oxidase FMS1 (EC 1.5.3.17)	protein	494	37% helix, 20% strand	P50264
B	Polyamine oxidase FMS1 (EC 1.5.3.17)	protein	502	38% helix, 20% strand	P50264
C	Polyamine oxidase FMS1 (EC 1.5.3.17)	protein	488	39% helix, 20% strand	P50264
D	Polyamine oxidase FMS1 (EC 1.5.3.17)	protein	498	37% helix, 19% strand	P50264

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
PG4 · Tetraethylene glycol · additive · 4 copies · chains A, B, C, D

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

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	648	0.88	0.93	94	FAD, PG4
2	657	0.88	0.92	96	FAD, PG4
3	445	0.87	0.94	82	FAD, PG4
4	434	0.87	0.94	83	FAD, PG4
5	336	0.65	0.80	45	empty

Interfaces

4 interfaces between chains.

C–D · 1573 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1571 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 488 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 410 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4GDP · Yeast polyamine oxidase FMS1, N195A mutant · the same entry in another collection · chain D against D, TM-score 1.00
P50264 · AlphaFold monomer V2.0 prediction for polyamine oxidase FMS1 (P50264) · a predicted model of the same protein · chain C 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 P50264
Elsewhere: RCSB PDB 4GDP · PDBe 4GDP · UniProt P50264

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