SMTL ID : 4wq2.1

Human calpain PEF(S) with (Z)-3-(6-bromondol-3-yl)-2-mercaptoacrylic acid bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

2 x 3SU: (2Z)-3-(6-bromo-1H-indol-3-yl)-2-sulfanylprop-2-enoic acid(Non-covalent)

3SU.1: 8 residues within 4Å: Chain A: L.29, V.32, V.33, H.36, L.39, I.76, Q.80, F.131 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.32, A:L.39, A:I.76, A:Q.80 Hydrogen bonds: A:Q.80 Salt bridges: A:H.36, A:K.84 3SU.8: 10 residues within 4Å: Chain B: L.29, V.32, V.33, H.36, L.39, W.73, I.76, Q.80, K.84, F.131 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.39, B:I.76, B:Q.80 Hydrogen bonds: B:Q.80, B:Q.80 Salt bridges: B:H.36, B:K.84

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: A.14, D.17, E.19, E.24 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.14, A:D.17, A:E.24, H2O.1, H2O.4 CA.3: 5 residues within 4Å: Chain A: D.57, D.59, T.61, K.63, E.68 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.57, A:D.59, A:T.61, A:K.63, H2O.2 CA.4: 5 residues within 4Å: Chain A: D.87, D.89, S.91, T.93, E.98 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.87, A:S.91, A:T.93, A:E.98, H2O.4 CA.5: 4 residues within 4Å: Chain A: D.42, D.130, D.132, N.133 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.42, A:D.130, A:D.132, H2O.3, H2O.4 CA.9: 4 residues within 4Å: Chain B: A.14, D.17, E.19, E.24 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.14, B:D.17, B:E.24, H2O.5, H2O.6 CA.10: 5 residues within 4Å: Chain B: D.57, D.59, T.61, K.63, E.68 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.57, B:D.59, B:T.61, B:K.63, H2O.5 CA.11: 5 residues within 4Å: Chain B: D.87, D.89, S.91, T.93, E.98 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.87, B:D.89, B:T.93, B:E.98, H2O.6 CA.12: 4 residues within 4Å: Chain B: D.42, D.130, D.132, N.133 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.42, B:D.130, B:D.132, H2O.6, H2O.6

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain A: E.2, F.6, W.73, N.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.74 EDO.7: 7 residues within 4Å: Chain A: R.50, V.53, A.54, G.62, Y.172 Chain B: R.120, R.121 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.50, A:R.50, A:Y.172, A:Y.172 EDO.13: 4 residues within 4Å: Chain B: Q.12, L.13, G.15, E.24 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.16, B:E.24, B:E.24 EDO.14: 5 residues within 4Å: Chain B: A.54, V.55, D.57, L.169, Y.172 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.54

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adams, S.E. et al., Conformationally restricted calpain inhibitors. Chem Sci (2015)

Release Date

2015-09-02

Peptides

Calpain small subunit 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Calpain small subunit 1

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