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Crystal structure of pea prolegumin, an 11S seed globulin from pisum sativum L.

Analyse Crystal structure of pea prolegumin, an 11S seed globulin from pisum sativum L. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KSC
Type: protein
Length: 2,274 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lega class
UniProt: Q9T0P5
Ligands: SO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 13% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lega class	protein	380	13% helix, 37% strand	Q9T0P5
B	Lega class	protein	383	12% helix, 37% strand	Q9T0P5
C	Lega class	protein	375	13% helix, 37% strand	Q9T0P5
D	Lega class	protein	376	13% helix, 38% strand	Q9T0P5
E	Lega class	protein	383	14% helix, 37% strand	Q9T0P5
F	Lega class	protein	377	14% helix, 37% strand	Q9T0P5

Ligands and binding sites

SO4 · Sulfate ion · ion · 13 copies · chains A, B, E, C, D
GOL · Glycerol · additive · 18 copies · chains A, B, E, C, D, 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1000	0.80	0.82	107	empty
2	254	0.72	0.86	31	empty
3	371	0.70	0.82	44	empty
4	397	0.69	0.81	49	empty
5	320	0.67	0.82	49	empty

Interfaces

7 interfaces between chains.

A–B · 2903 Å² buried · 39 hydrogen bonds · protein-protein
D–E · 2877 Å² buried · 38 hydrogen bonds · protein-protein
E–F · 2865 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 2753 Å² buried · 40 hydrogen bonds · protein-protein
B–C · 2717 Å² buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3KSC · Crystal structure of pea prolegumin, an 11S seed globulin from Pisum sativum L. · the same entry in another collection · 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 Q9T0P5
Elsewhere: RCSB PDB 3KSC · PDBe 3KSC · UniProt Q9T0P5

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