SMTL ID : 4aw9.1

Crystal structure of active legumain in complex with YVAD-CMK

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

ACE-TYR-VAL-ALA-ASP-0QE.1: 14 residues within 4Å: Chain A: R.19, H.20, D.122, H.123, G.124, E.162, C.164, S.191, Y.192, A.193, Y.203, D.206, W.207, T.239 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.192, A:Y.192, A:Y.203, A:Y.203, A:W.207, A:T.239 Hydrogen bonds: A:R.19, A:G.124, A:C.164, A:S.191, A:A.193, A:Y.203 Salt bridges: A:R.19, A:H.20 pi-Stacking: A:W.207

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

NAG.2: 7 residues within 4Å: Chain A: N.142, I.145, H.146, 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: 4 residues within 4Å: Chain A: K.156, D.175, N.176, N.247 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: N.66, D.197 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.200

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

SO4.5: 3 residues within 4Å: Chain A: H.227, H.231, Q.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.244 Salt bridges: A:H.227, A:H.231 SO4.6: 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 SO4.7: 1 residues within 4Å: Chain A: R.33 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dall, E. et al., Mechanistic and Structural Studies on Legumain Explain its Zymogenicity, Distinct Activation Pathways, and Regulation. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-06-26

Peptides

LEGUMAIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LEGUMAIN

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