SMTL ID : 7x79.1

The crystal structure of human Calpain-1 protease core in complex with 14b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 89K: N-[(2S)-3-cyclohexyl-1-oxidanylidene-1-[[(2S,3S)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide(Covalent)

89K.1: 19 residues within 4Å: Chain A: Q.109, L.112, G.113, D.114, C.115, W.116, S.206, G.207, G.208, T.210, S.251, M.260, E.261, G.271, H.272, A.273, W.298, E.349 Ligands: H2S.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.273 Hydrogen bonds: A:Q.109, A:C.115, A:G.207, A:G.208, A:G.208, A:E.261, A:E.261, A:G.271, A:H.272 Water bridges: A:E.261

1 x H2S: HYDROSULFURIC ACID(Covalent)

H2S.2: 5 residues within 4Å: Chain A: C.115, W.116, H.272, A.273 Ligands: 89K.1 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: V.99, G.101, D.106, E.185 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.99, A:G.101, A:D.106, A:E.185, H2O.2 CA.4: 5 residues within 4Å: Chain A: E.302, D.309, M.329, D.331, E.333 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.302, A:D.309, A:D.331, A:E.333, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., The crystal structure of human Calpain-1 protease core in complex with 14a. To Be Published

Release Date

2023-06-14

Peptides

Calpain-1 catalytic subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Calpain-1 catalytic subunit

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