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Crystal structure of plant vegetative storage protein

Analyse Crystal structure of plant vegetative storage protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FYP
Type: protein
Length: 449 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vegetative storage protein 1
UniProt: O49195
Ligands: MG
Pockets: 6 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vegetative storage protein 1	protein	228	44% helix, 14% strand	O49195
B	Vegetative storage protein 1	protein	221	43% helix, 15% strand	O49195

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

6 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	351	0.74	0.85	36	empty
2	377	0.66	0.80	36	MG
3	357	0.64	0.79	36	MG
4	135	0.45	0.77	28	empty
5	78	0.40	0.78	19	empty

Interfaces

1 interface between chains.

A–B · 1560 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4FYP · Crystal Structure of Plant Vegetative Storage Protein · the same entry in another collection · chain A against A, TM-score 1.00
O49195 · AlphaFold monomer V2.0 prediction for vegetative storage protein 1 (O49195) · a predicted model of the same protein · chain B 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 O49195
Elsewhere: RCSB PDB 4FYP · PDBe 4FYP · UniProt O49195

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