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Psao and xenon

Analyse Psao and xenon in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1W2Z
Type: protein
Length: 2,568 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amine oxidase, copper containing
EC: 1.4.3.6
UniProt: Q43077
Ligands: NAG, CU, MN, IOD, XE
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Amine oxidase, copper containing (EC 1.4.3.6)	protein	642	13% helix, 41% strand	Q43077

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
IOD · Iodide ion · ion · 176 copies · chains A, B, D, C
XE · Xenon · ion · 8 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	627	0.85	0.90	87	IOD
2	383	0.80	0.89	59	IOD
3	283	0.80	0.91	45	IOD
4	225	0.79	0.93	45	IOD
5	213	0.79	0.93	51	IOD

Interfaces

3 interfaces between chains.

C–D · 8071 Å² buried · 142 hydrogen bonds · protein-protein
A–B · 8025 Å² buried · 148 hydrogen bonds · protein-protein
B–D · 173 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 8 glycan, 4 modified (disulfide, N-glycosylation, nonstandard).

Compared structures

1W2Z · PSAO and Xenon · the same entry in another collection · chain D against D, TM-score 1.00
Q43077 · AlphaFold monomer V2.0 prediction for primary amine oxidase (Q43077) · 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 Q43077
Elsewhere: RCSB PDB 1W2Z · PDBe 1W2Z · UniProt Q43077

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