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Crystal structure of antheraea pernyi arylphorin

Analyse Crystal structure of antheraea pernyi arylphorin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GWJ
Type: protein
Length: 4,044 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arylphorin
UniProt: Q7Z1F8
Ligands: MAN, NAG, BMA, GLC
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Arylphorin	protein	674	42% helix, 19% strand	Q7Z1F8

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 48 copies · chains D, A, E, F, B, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, D, E, C, B, F
BMA · beta-D-mannopyranose · sugar · 6 copies
GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, D, B, F, C, E
FMT · Formic acid · additive · 6 copies · chains A, B, C, D, E, F

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	1048	0.86	0.87	105	empty
2	1189	0.85	0.86	142	empty
3	938	0.83	0.84	101	empty
4	174	0.82	0.97	45	empty
5	165	0.82	0.97	43	empty

Interfaces

12 interfaces between chains.

B–F · 2418 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 2393 Å² buried · 17 hydrogen bonds · protein-protein
C–E · 2376 Å² buried · 17 hydrogen bonds · protein-protein
D–F · 1207 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1201 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 glycan, 6 disulfide (N-glycosylation, disulfide).

Compared structures

3GWJ · Crystal structure of Antheraea pernyi arylphorin · the same entry in another collection · chain F against F, TM-score 1.00
Q7Z1F8 · AlphaFold monomer V2.0 prediction for arylphorin (Q7Z1F8) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q7Z1F8
Elsewhere: RCSB PDB 3GWJ · PDBe 3GWJ · UniProt Q7Z1F8

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