SMTL ID : 7uti.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-16-8-4-2-2-mer

Ligands

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

ADP.1: 22 residues within 4Å: Chain A: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.16, A:D.159, A:D.159, A:E.216, A:G.303, A:G.304, A:Y.308, A:K.338, A:K.338 Salt bridges: A:K.20, A:K.20 ADP.3: 22 residues within 4Å: Chain B: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.16, B:D.159, B:D.159, B:E.216, B:G.303, B:G.304, B:Y.308, B:K.338, B:K.338 Salt bridges: B:K.20, B:K.20 ADP.5: 22 residues within 4Å: Chain C: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.16, C:D.159, C:D.159, C:E.216, C:G.303, C:G.304, C:Y.308, C:K.338, C:K.338 Salt bridges: C:K.20, C:K.20 ADP.7: 22 residues within 4Å: Chain D: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:S.16, D:D.159, D:D.159, D:E.216, D:G.303, D:G.304, D:Y.308, D:K.338, D:K.338 Salt bridges: D:K.20, D:K.20 ADP.9: 22 residues within 4Å: Chain E: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:S.16, E:D.159, E:D.159, E:E.216, E:G.303, E:G.304, E:Y.308, E:K.338, E:K.338 Salt bridges: E:K.20, E:K.20 ADP.11: 22 residues within 4Å: Chain F: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:S.16, F:D.159, F:D.159, F:E.216, F:G.303, F:G.304, F:Y.308, F:K.338, F:K.338 Salt bridges: F:K.20, F:K.20 ADP.13: 22 residues within 4Å: Chain G: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:S.16, G:D.159, G:D.159, G:E.216, G:G.303, G:G.304, G:Y.308, G:K.338, G:K.338 Salt bridges: G:K.20, G:K.20 ADP.15: 22 residues within 4Å: Chain H: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.16 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:S.16, H:Q.139, H:D.159, H:D.159, H:E.216, H:G.303, H:G.304, H:Y.308, H:Y.308, H:K.338, H:K.338 Salt bridges: H:K.20, H:K.20 ADP.17: 22 residues within 4Å: Chain I: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.18 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:S.16, I:D.159, I:D.159, I:E.216, I:G.303, I:G.304, I:Y.308, I:Y.308, I:K.338, I:K.338 Salt bridges: I:K.20, I:K.20 ADP.19: 22 residues within 4Å: Chain J: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.20 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:S.16, J:D.159, J:D.159, J:E.216, J:G.303, J:G.304, J:Y.308, J:K.338, J:K.338 Salt bridges: J:K.20, J:K.20 ADP.21: 22 residues within 4Å: Chain K: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.22 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:S.16, K:D.159, K:D.159, K:E.216, K:G.303, K:G.304, K:Y.308, K:K.338, K:K.338 Salt bridges: K:K.20, K:K.20 ADP.23: 22 residues within 4Å: Chain L: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.24 11 PLIP interactions: 11 interactions with chain L Hydrogen bonds: L:S.16, L:D.159, L:D.159, L:E.216, L:G.303, L:G.304, L:Y.308, L:K.338, L:K.338 Salt bridges: L:K.20, L:K.20 ADP.25: 22 residues within 4Å: Chain M: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.26 11 PLIP interactions: 11 interactions with chain M Hydrogen bonds: M:S.16, M:D.159, M:D.159, M:E.216, M:G.303, M:G.304, M:Y.308, M:K.338, M:K.338 Salt bridges: M:K.20, M:K.20 ADP.27: 22 residues within 4Å: Chain N: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.28 11 PLIP interactions: 11 interactions with chain N Hydrogen bonds: N:S.16, N:D.159, N:D.159, N:E.216, N:G.303, N:G.304, N:Y.308, N:K.338, N:K.338 Salt bridges: N:K.20, N:K.20 ADP.29: 22 residues within 4Å: Chain O: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.30 11 PLIP interactions: 11 interactions with chain O Hydrogen bonds: O:S.16, O:D.159, O:D.159, O:E.216, O:G.303, O:G.304, O:Y.308, O:K.338, O:K.338 Salt bridges: O:K.20, O:K.20 ADP.31: 22 residues within 4Å: Chain P: D.13, G.15, S.16, G.17, L.18, K.20, Q.139, D.156, G.158, D.159, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338, V.341 Ligands: MG.32 11 PLIP interactions: 11 interactions with chain P Hydrogen bonds: P:S.16, P:D.159, P:D.159, P:E.216, P:G.303, P:G.304, P:Y.308, P:K.338, P:K.338 Salt bridges: P:K.20, P:K.20

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.156 MG.4: 6 residues within 4Å: Chain B: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.156 MG.6: 6 residues within 4Å: Chain C: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.156 MG.8: 6 residues within 4Å: Chain D: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.156 MG.10: 6 residues within 4Å: Chain E: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.156 MG.12: 6 residues within 4Å: Chain F: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.156 MG.14: 6 residues within 4Å: Chain G: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.156 MG.16: 6 residues within 4Å: Chain H: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.156 MG.18: 6 residues within 4Å: Chain I: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.156 MG.20: 6 residues within 4Å: Chain J: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.156 MG.22: 6 residues within 4Å: Chain K: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.156 MG.24: 6 residues within 4Å: Chain L: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.23 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.156 MG.26: 6 residues within 4Å: Chain M: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.25 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.156 MG.28: 6 residues within 4Å: Chain N: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.27 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.156 MG.30: 6 residues within 4Å: Chain O: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.29 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.156 MG.32: 6 residues within 4Å: Chain P: D.156, S.157, G.158, G.303, G.304 Ligands: ADP.31 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.156

6 x CA: CALCIUM ION(Non-covalent)

CA.33: 7 residues within 4Å: Chain X: D.65, D.67, S.69, T.71, V.72, D.73, E.76 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:D.65, X:D.67, X:S.69, X:T.71, X:E.76 CA.34: 8 residues within 4Å: Chain X: D.141, N.143, N.144, D.145, R.147, I.148, D.149, E.152 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:D.141, X:D.145, X:R.147, X:E.152, X:E.152 CA.35: 7 residues within 4Å: Chain X: D.105, N.107, D.109, Y.111, I.112, D.113, E.116 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:D.105, X:D.109, X:Y.111, X:E.116, X:E.116 CA.36: 7 residues within 4Å: Chain 5: D.65, D.67, S.69, T.71, V.72, D.73, E.76 5 PLIP interactions: 5 interactions with chain 5 Metal complexes: 5:D.65, 5:D.67, 5:S.69, 5:T.71, 5:E.76 CA.37: 8 residues within 4Å: Chain 5: D.141, N.143, N.144, D.145, R.147, I.148, D.149, E.152 5 PLIP interactions: 5 interactions with chain 5 Metal complexes: 5:D.141, 5:D.145, 5:R.147, 5:E.152, 5:E.152 CA.38: 7 residues within 4Å: Chain 5: D.105, N.107, D.109, Y.111, I.112, D.113, E.116 5 PLIP interactions: 5 interactions with chain 5 Metal complexes: 5:D.105, 5:D.109, 5:Y.111, 5:E.116, 5:E.116

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: ABCDEFGHIJKLMNOP
Tropomyosin alpha-1 chain: QRSTYZ01
Isoform 6 of Troponin T, cardiac muscle: UV23
Troponin I, cardiac muscle: W4
Troponin C, slow skeletal and cardiac muscles: X5

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

D
F

E
G

F
H

G
I

H
J

I
K

J
L

K
M

L
N

M
O

N
P

O
Q

P
R

Q
e

R
f

S
W

T
b

Y
i

Z
j

0
g

1
h

U
X

V
Y

2
c

3
d

W
V

4
a

X
U

5
Z

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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