SMTL ID : 5lu9.1

Crystal structure of YVAD-cmk bound human legumain (AEP) in complex with compound 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

1 x ACE- TYR- VAL- ALA- ASP- 0QE: AC-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE(Non-covalent)

ACE-TYR-VAL-ALA-ASP-0QE.1: 14 residues within 4Å: Chain A: R.19, H.20, N.122, H.123, G.124, E.162, A.163, C.164, S.191, Y.192, A.193, Y.203, D.206, W.207 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.192, A:A.193, A:Y.203, A:W.207 Hydrogen bonds: A:R.19, A:G.124, A:C.164, A:S.191, A:A.193, A:Y.203, A:Y.203 Salt bridges: A:R.19, A:H.20 pi-Stacking: A:W.207

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 6 residues within 4Å: Chain A: N.142, I.145, H.172, L.173, P.174, I.177 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.145, A:I.177 Water bridges: A:H.172 NAG.3: 5 residues within 4Å: Chain A: K.156, D.175, N.176, N.247, T.249 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.176 Hydrogen bonds: A:N.247, A:T.249

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: T.57, N.66, K.199, R.200 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.66, A:N.66 Salt bridges: A:K.199, A:R.200 SO4.5: 3 residues within 4Å: Chain A: T.225, H.227, K.228 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.225 Salt bridges: A:H.227

1 x 3Y7: 7-(morpholin-4-yl)-2,1,3-benzoxadiazol-4-amine(Non-covalent)

3Y7.6: 5 residues within 4Å: Chain A: H.227, H.231, Q.244, K.248, S.251 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.244, A:S.251 Water bridges: A:K.234 pi-Stacking: A:H.231 pi-Cation interactions: A:H.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Inhibition of delta-secretase improves cognitive functions in mouse models of Alzheimer's disease. Nat Commun (2017)

Release Date

2017-03-29

Peptides

Legumain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Legumain

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