SMTL ID : 7utl.1

ALTERNATIVE MODELING OF TROPOMYOSIN IN HUMAN CARDIAC THIN FILAMENT IN THE CALCIUM FREE STATE

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-18-8-4-2-2-mer

Ligands

18 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.16, A:S.16, A:Q.139, A:D.156, A:E.216, A:G.304, A:Y.308, A:Y.308 Salt bridges: A:K.20, A:K.20 ADP.3: 20 residues within 4Å: Chain B: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.16, B:S.16, B:Q.139, B:D.156, B:E.216, B:G.304, B:Y.308, B:Y.308 Salt bridges: B:K.20, B:K.20 ADP.5: 20 residues within 4Å: Chain C: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.16, C:S.16, C:Q.139, C:D.156, C:E.216, C:G.304, C:Y.308, C:Y.308 Salt bridges: C:K.20, C:K.20 ADP.7: 20 residues within 4Å: Chain D: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.8 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:S.16, D:S.16, D:Q.139, D:D.156, D:E.216, D:G.304, D:Y.308, D:Y.308 Salt bridges: D:K.20, D:K.20 ADP.9: 20 residues within 4Å: Chain E: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.10 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.16, E:S.16, E:Q.139, E:D.156, E:E.216, E:G.304, E:Y.308, E:Y.308 Salt bridges: E:K.20, E:K.20 ADP.11: 20 residues within 4Å: Chain F: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.12 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:S.16, F:S.16, F:Q.139, F:D.156, F:E.216, F:G.304, F:Y.308, F:Y.308 Salt bridges: F:K.20, F:K.20 ADP.13: 20 residues within 4Å: Chain G: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.14 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:S.16, G:S.16, G:Q.139, G:D.156, G:E.216, G:G.304, G:Y.308, G:Y.308 Salt bridges: G:K.20, G:K.20 ADP.15: 20 residues within 4Å: Chain H: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.16 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:S.16, H:S.16, H:Q.139, H:D.156, H:E.216, H:G.304, H:Y.308, H:Y.308 Salt bridges: H:K.20, H:K.20 ADP.17: 20 residues within 4Å: Chain I: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.18 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:S.16, I:S.16, I:Q.139, I:D.156, I:E.216, I:G.304, I:Y.308, I:Y.308 Salt bridges: I:K.20, I:K.20 ADP.19: 20 residues within 4Å: Chain J: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.20 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:S.16, J:S.16, J:Q.139, J:D.156, J:E.216, J:G.304, J:Y.308, J:Y.308 Salt bridges: J:K.20, J:K.20 ADP.21: 20 residues within 4Å: Chain K: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.22 10 PLIP interactions: 10 interactions with chain K Hydrogen bonds: K:S.16, K:S.16, K:Q.139, K:D.156, K:E.216, K:G.304, K:Y.308, K:Y.308 Salt bridges: K:K.20, K:K.20 ADP.23: 20 residues within 4Å: Chain L: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.24 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:S.16, L:S.16, L:Q.139, L:D.156, L:E.216, L:G.304, L:Y.308, L:Y.308 Salt bridges: L:K.20, L:K.20 ADP.25: 20 residues within 4Å: Chain M: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.26 10 PLIP interactions: 10 interactions with chain M Hydrogen bonds: M:S.16, M:S.16, M:Q.139, M:D.156, M:E.216, M:G.304, M:Y.308, M:Y.308 Salt bridges: M:K.20, M:K.20 ADP.27: 20 residues within 4Å: Chain N: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.28 10 PLIP interactions: 10 interactions with chain N Hydrogen bonds: N:S.16, N:S.16, N:Q.139, N:D.156, N:E.216, N:G.304, N:Y.308, N:Y.308 Salt bridges: N:K.20, N:K.20 ADP.29: 20 residues within 4Å: Chain O: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.30 10 PLIP interactions: 10 interactions with chain O Hydrogen bonds: O:S.16, O:S.16, O:Q.139, O:D.156, O:E.216, O:G.304, O:Y.308, O:Y.308 Salt bridges: O:K.20, O:K.20 ADP.31: 20 residues within 4Å: Chain P: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.32 10 PLIP interactions: 10 interactions with chain P Hydrogen bonds: P:S.16, P:S.16, P:Q.139, P:D.156, P:E.216, P:G.304, P:Y.308, P:Y.308 Salt bridges: P:K.20, P:K.20 ADP.33: 20 residues within 4Å: Chain Q: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.34 10 PLIP interactions: 10 interactions with chain Q Hydrogen bonds: Q:S.16, Q:S.16, Q:Q.139, Q:D.156, Q:E.216, Q:G.304, Q:Y.308, Q:Y.308 Salt bridges: Q:K.20, Q:K.20 ADP.35: 20 residues within 4Å: Chain R: G.15, S.16, G.17, L.18, K.20, Q.139, D.156, S.157, G.158, D.159, G.184, R.212, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.36 10 PLIP interactions: 10 interactions with chain R Hydrogen bonds: R:S.16, R:S.16, R:Q.139, R:D.156, R:E.216, R:G.304, R:Y.308, R:Y.308 Salt bridges: R:K.20, R:K.20

18 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.156, S.157, G.158, G.303 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.156 MG.4: 5 residues within 4Å: Chain B: D.156, S.157, G.158, G.303 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.156 MG.6: 5 residues within 4Å: Chain C: D.156, S.157, G.158, G.303 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.156 MG.8: 5 residues within 4Å: Chain D: D.156, S.157, G.158, G.303 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.156 MG.10: 5 residues within 4Å: Chain E: D.156, S.157, G.158, G.303 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.156 MG.12: 5 residues within 4Å: Chain F: D.156, S.157, G.158, G.303 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.156 MG.14: 5 residues within 4Å: Chain G: D.156, S.157, G.158, G.303 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.156 MG.16: 5 residues within 4Å: Chain H: D.156, S.157, G.158, G.303 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.156 MG.18: 5 residues within 4Å: Chain I: D.156, S.157, G.158, G.303 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.156 MG.20: 5 residues within 4Å: Chain J: D.156, S.157, G.158, G.303 Ligands: ADP.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.156 MG.22: 5 residues within 4Å: Chain K: D.156, S.157, G.158, G.303 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.156 MG.24: 5 residues within 4Å: Chain L: D.156, S.157, G.158, G.303 Ligands: ADP.23 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.156 MG.26: 5 residues within 4Å: Chain M: D.156, S.157, G.158, G.303 Ligands: ADP.25 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.156 MG.28: 5 residues within 4Å: Chain N: D.156, S.157, G.158, G.303 Ligands: ADP.27 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.156 MG.30: 5 residues within 4Å: Chain O: D.156, S.157, G.158, G.303 Ligands: ADP.29 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.156 MG.32: 5 residues within 4Å: Chain P: D.156, S.157, G.158, G.303 Ligands: ADP.31 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.156 MG.34: 5 residues within 4Å: Chain Q: D.156, S.157, G.158, G.303 Ligands: ADP.33 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:D.156 MG.36: 5 residues within 4Å: Chain R: D.156, S.157, G.158, G.303 Ligands: ADP.35 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:D.156

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pavadai, E. et al., Protein-Protein Docking Reveals Dynamic Interactions of Tropomyosin on Actin Filaments. Biophys J (2020)

Release Date

2022-09-21

Peptides

Actin, alpha skeletal muscle: ABCDEFGHIJKLMNOPQR
Tropomyosin alpha-1 chain: STUV0123
Isoform 6 of Troponin T, cardiac muscle: WX45
Troponin I, cardiac muscle: Y6
Troponin C, slow skeletal and cardiac muscles: Z7

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
a

T
b

U
W

V
Z

0
i

1
j

2
g

3
h

W
X

X
Y

4
e

5
f

Y
V

6
c

Z
U

7
d

Actin, alpha skeletal muscle

Tropomyosin alpha-1 chain

Isoform 6 of Troponin T, cardiac muscle

Troponin I, cardiac muscle

Troponin C, slow skeletal and cardiac muscles

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