MolNFT v1 · #183849 · protein

Crystal structure of human legumain in complex with gly-ser-asn peptide

7O50: “Crystal structure of human legumain in complex with gly-ser-asn peptide”. X-ray diffraction, 3 ligands (SNN, ACE, NAG), 3 pockets (best druggability 0.40). MolNFT v1 #183849 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7O50
Type: protein
Length: 528 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Legumain; Gly-ser-asn
EC: 3.4.22.34
UniProt: Q99538
Ligands: SNN, ACE, NAG
Pockets: 3 · best druggability 0.40

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Legumain (EC 3.4.22.34)	protein	261	33% helix, 20% strand	Q99538
H, C	Gly-ser-asn	protein	3	0% helix, 33% strand	—

Ligands and binding sites

SNN · L-3-aminosuccinimide · ligand · 2 copies · chains A, H, B, C
ACE · Acetyl group · ligand · 2 copies · chains A, B, H, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	142	0.40	0.74	24	empty
2	138	0.39	0.73	19	empty
3	60	0.33	0.77	17	empty

Interfaces

5 interfaces between chains.

A–B · 605 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 267 Å² buried · 14 hydrogen bonds · protein-protein
A–H · 265 Å² buried · 13 hydrogen bonds · protein-protein
B–H · 86 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 17 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent, 5 glycan (covalent ligand, N-glycosylation).

Compared structures

7O50 · Crystal structure of human legumain in complex with Gly-Ser-Asn peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q99538 · AlphaFold monomer V2.0 prediction for legumain (Q99538) · 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 Q99538
Elsewhere: RCSB PDB 7O50 · PDBe 7O50 · UniProt Q99538

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