SMTL ID : 3rv5.5 (4 other biounits)

Crystal structure of human cardiac troponin C regulatory domain in complex with cadmium and deoxycholic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

42 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: G.30, D.33, C.35, E.40 Ligand excluded by PLIP CD.2: 5 residues within 4Å: Chain A: D.65, D.67, S.69, T.71, E.76 Ligand excluded by PLIP CD.3: 1 residues within 4Å: Chain A: C.35 Ligand excluded by PLIP CD.4: 2 residues within 4Å: Chain A: D.73, D.75 Ligand excluded by PLIP CD.5: 2 residues within 4Å: Chain A: E.66 Chain B: E.32 Ligand excluded by PLIP CD.11: 5 residues within 4Å: Chain B: G.30, D.33, C.35, E.40 Ligands: CD.13 Ligand excluded by PLIP CD.12: 5 residues within 4Å: Chain B: D.65, D.67, S.69, T.71, E.76 Ligand excluded by PLIP CD.13: 3 residues within 4Å: Chain B: D.33, C.35 Ligands: CD.11 Ligand excluded by PLIP CD.14: 2 residues within 4Å: Chain B: D.73, D.75 Ligand excluded by PLIP CD.15: 1 residues within 4Å: Chain B: E.32 Ligand excluded by PLIP CD.16: 2 residues within 4Å: Chain B: E.59 Ligands: DXC.23 Ligand excluded by PLIP CD.17: 2 residues within 4Å: Chain B: D.62 Chain C: E.14 Ligand excluded by PLIP CD.18: 4 residues within 4Å: Chain C: G.30, D.33, C.35, E.40 Ligand excluded by PLIP CD.19: 5 residues within 4Å: Chain C: D.65, D.67, S.69, T.71, E.76 Ligand excluded by PLIP CD.20: 1 residues within 4Å: Chain C: C.35 Ligand excluded by PLIP CD.21: 2 residues within 4Å: Chain C: D.73, D.75 Ligand excluded by PLIP CD.22: 2 residues within 4Å: Chain C: E.66 Chain D: E.32 Ligand excluded by PLIP CD.28: 5 residues within 4Å: Chain D: G.30, D.33, C.35, E.40 Ligands: CD.30 Ligand excluded by PLIP CD.29: 5 residues within 4Å: Chain D: D.65, D.67, S.69, T.71, E.76 Ligand excluded by PLIP CD.30: 3 residues within 4Å: Chain D: D.33, C.35 Ligands: CD.28 Ligand excluded by PLIP CD.31: 2 residues within 4Å: Chain D: D.73, D.75 Ligand excluded by PLIP CD.32: 1 residues within 4Å: Chain D: E.32 Ligand excluded by PLIP CD.33: 2 residues within 4Å: Chain D: E.59 Ligands: DXC.6 Ligand excluded by PLIP CD.34: 2 residues within 4Å: Chain A: E.14 Chain D: D.62 Ligand excluded by PLIP CD.35: 5 residues within 4Å: Chain E: G.30, D.33, C.35, E.40 Ligands: CD.37 Ligand excluded by PLIP CD.36: 5 residues within 4Å: Chain E: D.65, D.67, S.69, T.71, E.76 Ligand excluded by PLIP CD.37: 3 residues within 4Å: Chain E: D.33, C.35 Ligands: CD.35 Ligand excluded by PLIP CD.38: 2 residues within 4Å: Chain E: D.73, D.75 Ligand excluded by PLIP CD.39: 3 residues within 4Å: Chain E: E.59 Chain H: E.10 Ligands: DXC.58 Ligand excluded by PLIP CD.42: 4 residues within 4Å: Chain F: G.30, D.33, C.35, E.40 Ligand excluded by PLIP CD.43: 5 residues within 4Å: Chain F: D.65, D.67, S.69, T.71, E.76 Ligand excluded by PLIP CD.44: 2 residues within 4Å: Chain F: D.33, C.35 Ligand excluded by PLIP CD.45: 3 residues within 4Å: Chain F: D.67, D.73, D.75 Ligand excluded by PLIP CD.47: 5 residues within 4Å: Chain G: G.30, D.33, C.35, E.40 Ligands: CD.49 Ligand excluded by PLIP CD.48: 5 residues within 4Å: Chain G: D.65, D.67, S.69, T.71, E.76 Ligand excluded by PLIP CD.49: 3 residues within 4Å: Chain G: D.33, C.35 Ligands: CD.47 Ligand excluded by PLIP CD.50: 2 residues within 4Å: Chain G: D.73, D.75 Ligand excluded by PLIP CD.51: 3 residues within 4Å: Chain F: E.10 Chain G: E.59 Ligands: DXC.46 Ligand excluded by PLIP CD.54: 4 residues within 4Å: Chain H: G.30, D.33, C.35, E.40 Ligand excluded by PLIP CD.55: 5 residues within 4Å: Chain H: D.65, D.67, S.69, T.71, E.76 Ligand excluded by PLIP CD.56: 2 residues within 4Å: Chain H: D.33, C.35 Ligand excluded by PLIP CD.57: 3 residues within 4Å: Chain H: D.67, D.73, D.75 Ligand excluded by PLIP

10 x DXC: (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID(Non-covalent)

DXC.6: 9 residues within 4Å: Chain A: K.17, F.20, K.21, F.24 Chain B: V.82 Chain D: E.59 Chain E: I.4, Y.5 Ligands: CD.33 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: A:K.17, A:F.20, A:F.24, B:V.82, B:V.82, E:I.4 Salt bridges: A:K.17 DXC.7: 6 residues within 4Å: Chain A: V.79, V.82, R.83 Chain B: K.17, F.20, K.21 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:K.17, B:F.20, A:V.82, A:V.82 Salt bridges: A:R.83 DXC.8: 8 residues within 4Å: Chain A: F.27, M.45, Q.50, F.77, M.80 Chain B: M.81 Chain E: D.3, I.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.27, A:F.27, A:F.77, A:F.77 Hydrogen bonds: A:Q.50 DXC.23: 9 residues within 4Å: Chain B: E.59 Chain C: K.17, F.20, K.21, F.24 Chain D: V.82 Chain G: I.4, Y.5 Ligands: CD.16 7 PLIP interactions: 4 interactions with chain C, 1 interactions with chain G, 2 interactions with chain D Hydrophobic interactions: C:K.17, C:F.20, C:F.24, G:I.4, D:V.82, D:V.82 Salt bridges: C:K.17 DXC.24: 6 residues within 4Å: Chain C: V.79, V.82, R.83 Chain D: K.17, F.20, K.21 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:K.17, D:F.20, C:V.82, C:V.82 Salt bridges: C:R.83 DXC.25: 8 residues within 4Å: Chain C: F.27, M.45, Q.50, F.77, M.80 Chain D: M.81 Chain G: D.3, I.4 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.27, C:F.27, C:F.77, C:F.77 Hydrogen bonds: C:Q.50 DXC.41: 6 residues within 4Å: Chain A: I.4 Chain E: V.9, F.20, K.21, F.24 Chain F: V.82 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: E:V.9, E:F.20, E:F.24, F:V.82, A:I.4 DXC.46: 9 residues within 4Å: Chain B: Y.5 Chain E: V.82 Chain F: E.10, K.17, F.20, K.21, F.24 Chain G: E.59 Ligands: CD.51 12 PLIP interactions: 7 interactions with chain F, 2 interactions with chain E, 3 interactions with chain B Hydrophobic interactions: F:F.20, F:K.21, F:F.24, F:F.24, F:F.24, E:V.82, E:V.82, B:Y.5, B:Y.5, B:Y.5 Hydrogen bonds: F:E.10 Salt bridges: F:K.17 DXC.53: 6 residues within 4Å: Chain C: I.4 Chain G: V.9, F.20, K.21, F.24 Chain H: V.82 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: G:V.9, G:F.20, G:F.24, H:V.82, C:I.4 DXC.58: 9 residues within 4Å: Chain D: Y.5 Chain E: E.59 Chain G: V.82 Chain H: E.10, K.17, F.20, K.21, F.24 Ligands: CD.39 12 PLIP interactions: 3 interactions with chain D, 2 interactions with chain G, 7 interactions with chain H Hydrophobic interactions: D:Y.5, D:Y.5, D:Y.5, G:V.82, G:V.82, H:F.20, H:K.21, H:F.24, H:F.24, H:F.24 Hydrogen bonds: H:E.10 Salt bridges: H:K.17

6 x CA: CALCIUM ION(Non-covalent)

CA.9: 2 residues within 4Å: Chain A: E.32 Chain B: E.66 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.66 CA.10: 2 residues within 4Å: Chain B: E.59, E.63 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.59, B:E.63, H2O.75 CA.26: 2 residues within 4Å: Chain C: E.32 Chain D: E.66 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.66 CA.27: 2 residues within 4Å: Chain D: E.59, E.63 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.59, D:E.63, H2O.155 CA.40: 2 residues within 4Å: Chain E: E.32 Chain F: D.75 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Metal complexes: F:D.75, E:E.32 CA.52: 2 residues within 4Å: Chain G: E.32 Chain H: D.75 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Metal complexes: H:D.75, G:E.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, A.Y. et al., Crystal structure of cardiac troponin C regulatory domain in complex with cadmium and deoxycholic Acid reveals novel conformation. J.Mol.Biol. (2011)

Release Date

2011-08-31

Peptides

Troponin C, slow skeletal and cardiac muscles: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
C

F
D

G
C

H
D

Troponin C, slow skeletal and cardiac muscles

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