MolNFT v1 · #16921 · protein

Crystal structure of glycinin A3B4 subunit homohexamer

1OD5: “Crystal structure of glycinin A3B4 subunit homohexamer”. X-ray diffraction, 2 ligands (MG, CO3), 7 pockets (best druggability 0.77). MolNFT v1 #16921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1OD5
Type: protein
Length: 764 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycinin
UniProt: Q39922
Ligands: MG, CO3
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glycinin	protein	382	14% helix, 38% strand	Q39922

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains B, A
CO3 · Carbonate ion · ion · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	331	0.77	0.89	52	empty
2	121	0.46	0.78	17	empty
3	78	0.42	0.79	19	empty
4	71	0.32	0.75	18	empty
5	71	0.30	0.74	19	empty

Interfaces

1 interface between chains.

A–B · 2171 Å² buried · 35 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1OD5 · Crystal structure of glycinin A3B4 subunit homohexamer · 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 Q39922
Elsewhere: RCSB PDB 1OD5 · PDBe 1OD5 · UniProt Q39922

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