MolNFT v1 · #23859 · protein

Crystal structure of proglycinin mutant C88S

1UD1 · Glycinin G1: “Crystal structure of proglycinin mutant C88S”. X-ray diffraction, 5 pockets (best druggability 0.75). MolNFT v1 #23859 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1UD1
Type: protein
Length: 1,098 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycinin G1
UniProt: P04776
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Glycinin G1	protein	366	14% helix, 37% strand	P04776

Pockets

5 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	897	0.75	0.79	72	empty
2	122	0.42	0.76	23	empty
3	120	0.41	0.76	24	empty
4	100	0.39	0.76	19	empty
5	60	0.33	0.77	14	empty

Interfaces

3 interfaces between chains.

B–C · 2783 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 2755 Å² buried · 39 hydrogen bonds · protein-protein
A–C · 2745 Å² buried · 38 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1UD1 · Crystal structure of proglycinin mutant C88S · the same entry in another collection · chain A against A, TM-score 1.00
P04776 · AlphaFold monomer V2.0 prediction for glycinin G1 (P04776) · a predicted model of the same protein · chain A 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 P04776
Elsewhere: RCSB PDB 1UD1 · PDBe 1UD1 · UniProt P04776

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