MolNFT v1 · #88730 · protein

The structure of inactive prolegumain from chinese hamster.

4D3Y: “The structure of inactive prolegumain from chinese hamster.”. X-ray diffraction, 2 ligands (SNN, NAG), 3 pockets (best druggability 0.55). MolNFT v1 #88730 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4D3Y
Type: protein
Length: 385 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Legumain
EC: 3.4.22.34
UniProt: G3I1H5
Ligands: SNN, NAG
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Legumain (EC 3.4.22.34)	protein	385	44% helix, 15% strand	G3I1H5

Ligands and binding sites

SNN · L-3-aminosuccinimide · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
GOL · Glycerol · additive · chains A

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

Pockets

3 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	137	0.55	0.82	23	empty
2	94	0.43	0.79	17	empty
3	75	0.32	0.74	15	empty

Modifications

Observed in the structure: 3 glycan, 2 covalent, 2 disulfide, 1 modified (N-glycosylation, covalent ligand, disulfide, oxidation).

Compared structures

4D3Y · The structure of inactive prolegumain from chinese hamster. · 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 G3I1H5
Elsewhere: RCSB PDB 4D3Y · PDBe 4D3Y · UniProt G3I1H5

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