SMTL ID : 6izr.1

Whole structure of a 15-stranded ParM filament from Clostridium botulinum

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-30-mer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, V.315, E.335 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.12, A:G.13, A:Q.14, A:Q.14, A:F.198, A:Y.233, A:E.260, A:E.260, A:G.311, A:G.312 Salt bridges: A:K.16, A:K.16 ADP.3: 17 residues within 4Å: Chain B: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, V.315, E.335 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.12, B:G.13, B:Q.14, B:Q.14, B:F.198, B:Y.233, B:E.260, B:E.260, B:G.311, B:G.312 Salt bridges: B:K.16, B:K.16 ADP.5: 19 residues within 4Å: Chain C: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.13, C:Q.14, C:Q.14, C:Q.14, C:F.198, C:Y.233, C:Y.233, C:G.311, C:K.314, C:K.314 Salt bridges: C:K.16, C:K.16 ADP.7: 19 residues within 4Å: Chain D: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.13, D:Q.14, D:Q.14, D:Q.14, D:F.198, D:Y.233, D:G.311, D:K.314, D:E.335 Salt bridges: D:K.16, D:K.16 ADP.9: 19 residues within 4Å: Chain E: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.13, E:Q.14, E:Q.14, E:Q.14, E:F.198, E:Y.233, E:G.311, E:K.314, E:E.335 Salt bridges: E:K.16, E:K.16 ADP.11: 19 residues within 4Å: Chain F: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315 Ligands: MG.12 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.13, F:Q.14, F:Q.14, F:Q.14, F:F.198, F:Y.233, F:Y.233, F:G.311, F:K.314, F:K.314 Salt bridges: F:K.16, F:K.16 ADP.13: 19 residues within 4Å: Chain G: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:G.13, G:Q.14, G:Q.14, G:Q.14, G:F.198, G:Y.233, G:Y.233, G:G.311, G:K.314, G:K.314 Salt bridges: G:K.16, G:K.16 ADP.15: 18 residues within 4Å: Chain H: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315 Ligands: MG.16 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:G.11, H:G.13, H:Q.14, H:Q.14, H:Q.14, H:F.198, H:Y.233, H:G.311, H:G.312, H:K.314, H:K.314, H:E.335 Salt bridges: H:K.16, H:K.16 ADP.17: 18 residues within 4Å: Chain I: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315 Ligands: MG.18 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:G.13, I:Q.14, I:Q.14, I:Q.14, I:F.198, I:Y.233, I:G.311, I:G.312, I:K.314, I:K.314, I:E.335 Salt bridges: I:K.16, I:K.16 ADP.19: 19 residues within 4Å: Chain J: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, E.335 Ligands: MG.20 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:G.13, J:Q.14, J:Q.14, J:Q.14, J:F.198, J:Y.233, J:G.311, J:K.314, J:E.335 Salt bridges: J:K.16, J:K.16 ADP.21: 19 residues within 4Å: Chain K: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, E.335 Ligands: MG.22 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:G.13, K:Q.14, K:Q.14, K:Q.14, K:F.198, K:Y.233, K:G.311, K:K.314, K:E.335 Salt bridges: K:K.16, K:K.16 ADP.23: 17 residues within 4Å: Chain L: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, E.335 Ligands: MG.24 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:G.13, L:Q.14, L:Q.14, L:Q.14, L:F.198, L:Y.233, L:G.311, L:E.335 Salt bridges: L:K.16, L:K.16 ADP.25: 17 residues within 4Å: Chain M: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, E.335 Ligands: MG.26 10 PLIP interactions: 10 interactions with chain M Hydrogen bonds: M:G.13, M:Q.14, M:Q.14, M:Q.14, M:F.198, M:Y.233, M:G.311, M:E.335 Salt bridges: M:K.16, M:K.16 ADP.27: 19 residues within 4Å: Chain N: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315 Ligands: MG.28 12 PLIP interactions: 12 interactions with chain N Hydrogen bonds: N:G.13, N:Q.14, N:Q.14, N:Q.14, N:F.198, N:Y.233, N:Y.233, N:G.311, N:K.314, N:K.314 Salt bridges: N:K.16, N:K.16 ADP.29: 18 residues within 4Å: Chain O: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, V.315, E.335 Ligands: MG.30 9 PLIP interactions: 9 interactions with chain O Hydrogen bonds: O:Y.12, O:G.13, O:Q.14, O:F.198, O:Y.233, O:G.311, O:K.314 Salt bridges: O:K.16, O:K.16 ADP.31: 19 residues within 4Å: Chain P: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, K.314, V.315, E.335 Ligands: MG.32 15 PLIP interactions: 15 interactions with chain P Hydrogen bonds: P:Y.12, P:G.13, P:Q.14, P:Q.14, P:Q.168, P:F.198, P:Y.233, P:Y.233, P:E.260, P:G.311, P:G.312, P:K.314, P:K.314 Salt bridges: P:K.16, P:K.16 ADP.33: 17 residues within 4Å: Chain Q: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, V.315, E.335 Ligands: MG.34 10 PLIP interactions: 10 interactions with chain Q Hydrogen bonds: Q:Y.12, Q:G.13, Q:Q.14, Q:Q.14, Q:F.198, Q:Y.233, Q:Y.233, Q:G.311 Salt bridges: Q:K.16, Q:K.16 ADP.35: 18 residues within 4Å: Chain R: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, V.315, E.335 Ligands: MG.36 9 PLIP interactions: 9 interactions with chain R Hydrogen bonds: R:Y.12, R:G.13, R:Q.14, R:F.198, R:Y.233, R:G.311, R:K.314 Salt bridges: R:K.16, R:K.16 ADP.37: 19 residues within 4Å: Chain S: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, K.314, V.315, E.335 Ligands: MG.38 11 PLIP interactions: 11 interactions with chain S Hydrogen bonds: S:Y.12, S:G.13, S:Q.14, S:Q.14, S:F.198, S:Y.233, S:G.311, S:K.314, S:K.314 Salt bridges: S:K.16, S:K.16 ADP.39: 17 residues within 4Å: Chain T: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, V.315, E.335 Ligands: MG.40 10 PLIP interactions: 10 interactions with chain T Hydrogen bonds: T:Y.12, T:G.13, T:Q.14, T:Q.14, T:F.198, T:Y.233, T:Y.233, T:G.311 Salt bridges: T:K.16, T:K.16 ADP.41: 19 residues within 4Å: Chain U: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315, E.335 Ligands: MG.42 11 PLIP interactions: 11 interactions with chain U Hydrogen bonds: U:G.13, U:Q.14, U:F.198, U:Y.233, U:Y.233, U:E.260, U:G.311, U:G.312, U:K.314 Salt bridges: U:K.16, U:K.16 ADP.43: 19 residues within 4Å: Chain V: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, K.314, V.315, E.335 Ligands: MG.44 11 PLIP interactions: 11 interactions with chain V Hydrogen bonds: V:Y.12, V:G.13, V:Q.14, V:Q.14, V:F.198, V:Y.233, V:G.311, V:K.314, V:K.314 Salt bridges: V:K.16, V:K.16 ADP.45: 18 residues within 4Å: Chain W: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, K.314, V.315 Ligands: MG.46 13 PLIP interactions: 13 interactions with chain W Hydrogen bonds: W:D.9, W:Y.12, W:G.13, W:Q.14, W:Q.168, W:F.198, W:Y.233, W:E.260, W:G.311, W:K.314, W:K.314 Salt bridges: W:K.16, W:K.16 ADP.47: 19 residues within 4Å: Chain X: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315, E.335 Ligands: MG.48 11 PLIP interactions: 11 interactions with chain X Hydrogen bonds: X:G.13, X:Q.14, X:F.198, X:Y.233, X:Y.233, X:E.260, X:G.311, X:G.312, X:K.314 Salt bridges: X:K.16, X:K.16 ADP.49: 18 residues within 4Å: Chain Y: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, K.314, V.315, E.335 Ligands: MG.50 13 PLIP interactions: 13 interactions with chain Y Hydrogen bonds: Y:Y.12, Y:G.13, Y:G.13, Y:Q.14, Y:F.198, Y:Y.233, Y:Y.233, Y:G.311, Y:G.312, Y:K.314, Y:K.314 Salt bridges: Y:K.16, Y:K.16 ADP.51: 18 residues within 4Å: Chain Z: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, K.314, V.315 Ligands: MG.52 11 PLIP interactions: 11 interactions with chain Z Hydrogen bonds: Z:Y.12, Z:G.13, Z:Q.14, Z:F.198, Z:Y.233, Z:E.260, Z:G.311, Z:K.314, Z:K.314 Salt bridges: Z:K.16, Z:K.16 ADP.53: 19 residues within 4Å: Chain 0: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315, E.335 Ligands: MG.54 10 PLIP interactions: 10 interactions with chain 0 Hydrogen bonds: 0:G.13, 0:Q.14, 0:Q.14, 0:F.198, 0:Y.233, 0:G.311, 0:K.314, 0:K.314 Salt bridges: 0:K.16, 0:K.16 ADP.55: 18 residues within 4Å: Chain 1: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, K.314, V.315, E.335 Ligands: MG.56 13 PLIP interactions: 13 interactions with chain 1 Hydrogen bonds: 1:Y.12, 1:G.13, 1:G.13, 1:Q.14, 1:F.198, 1:Y.233, 1:Y.233, 1:G.311, 1:G.312, 1:K.314, 1:K.314 Salt bridges: 1:K.16, 1:K.16 ADP.57: 19 residues within 4Å: Chain 2: D.9, G.11, Y.12, G.13, Q.14, K.16, Q.168, G.197, F.198, M.229, Y.233, E.260, G.310, G.311, G.312, K.314, V.315, E.335 Ligands: MG.58 15 PLIP interactions: 15 interactions with chain 2 Hydrogen bonds: 2:Y.12, 2:G.13, 2:Q.14, 2:Q.14, 2:Q.168, 2:F.198, 2:Y.233, 2:Y.233, 2:E.260, 2:G.311, 2:G.312, 2:K.314, 2:K.314 Salt bridges: 2:K.16, 2:K.16 ADP.59: 19 residues within 4Å: Chain 3: D.9, G.11, Y.12, G.13, Q.14, K.16, G.197, F.198, M.229, Y.233, C.259, E.260, G.310, G.311, G.312, K.314, V.315, E.335 Ligands: MG.60 10 PLIP interactions: 10 interactions with chain 3 Hydrogen bonds: 3:G.13, 3:Q.14, 3:Q.14, 3:F.198, 3:Y.233, 3:G.311, 3:K.314, 3:K.314 Salt bridges: 3:K.16, 3:K.16

30 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.168, D.195, N.338 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.195 MG.4: 4 residues within 4Å: Chain B: Q.168, D.195, N.338 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.195 MG.6: 4 residues within 4Å: Chain C: Q.168, D.195, N.338 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.195 MG.8: 5 residues within 4Å: Chain D: D.9, Q.168, D.195, N.338 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.195 MG.10: 5 residues within 4Å: Chain E: D.9, Q.168, D.195, N.338 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.195 MG.12: 5 residues within 4Å: Chain F: D.9, Q.168, D.195, N.338 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 5 residues within 4Å: Chain G: D.9, Q.168, D.195, N.338 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain H: Q.168, D.195, N.338 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.195 MG.18: 4 residues within 4Å: Chain I: Q.168, D.195, N.338 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.195 MG.20: 4 residues within 4Å: Chain J: Q.168, D.195, N.338 Ligands: ADP.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.195 MG.22: 4 residues within 4Å: Chain K: Q.168, D.195, N.338 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.195 MG.24: 4 residues within 4Å: Chain L: D.9, D.195, N.338 Ligands: ADP.23 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.195 MG.26: 4 residues within 4Å: Chain M: D.9, D.195, N.338 Ligands: ADP.25 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.195 MG.28: 4 residues within 4Å: Chain N: Q.168, D.195, N.338 Ligands: ADP.27 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.195 MG.30: 4 residues within 4Å: Chain O: Q.168, D.195, N.338 Ligands: ADP.29 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:D.195 MG.32: 4 residues within 4Å: Chain P: Q.168, D.195, N.338 Ligands: ADP.31 1 PLIP interactions: 1 interactions with chain P Metal complexes: P:D.195 MG.34: 5 residues within 4Å: Chain Q: D.9, Q.168, D.195, N.338 Ligands: ADP.33 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:D.195 MG.36: 4 residues within 4Å: Chain R: Q.168, D.195, N.338 Ligands: ADP.35 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:D.195 MG.38: 6 residues within 4Å: Chain S: D.9, K.16, Q.168, D.195, N.338 Ligands: ADP.37 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:D.195 MG.40: 5 residues within 4Å: Chain T: D.9, Q.168, D.195, N.338 Ligands: ADP.39 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:D.195 MG.42: 4 residues within 4Å: Chain U: D.9, K.16, D.195 Ligands: ADP.41 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:D.195 MG.44: 6 residues within 4Å: Chain V: D.9, K.16, Q.168, D.195, N.338 Ligands: ADP.43 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:D.195 MG.46: 5 residues within 4Å: Chain W: D.9, Q.168, D.195, N.338 Ligands: ADP.45 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:D.195 MG.48: 4 residues within 4Å: Chain X: D.9, K.16, D.195 Ligands: ADP.47 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:D.195 MG.50: 4 residues within 4Å: Chain Y: Q.168, D.195, N.338 Ligands: ADP.49 1 PLIP interactions: 1 interactions with chain Y Metal complexes: Y:D.195 MG.52: 5 residues within 4Å: Chain Z: D.9, Q.168, D.195, N.338 Ligands: ADP.51 1 PLIP interactions: 1 interactions with chain Z Metal complexes: Z:D.195 MG.54: 5 residues within 4Å: Chain 0: D.9, Q.168, D.195, N.338 Ligands: ADP.53 1 PLIP interactions: 1 interactions with chain 0 Metal complexes: 0:D.195 MG.56: 4 residues within 4Å: Chain 1: Q.168, D.195, N.338 Ligands: ADP.55 1 PLIP interactions: 1 interactions with chain 1 Metal complexes: 1:D.195 MG.58: 4 residues within 4Å: Chain 2: Q.168, D.195, N.338 Ligands: ADP.57 1 PLIP interactions: 1 interactions with chain 2 Metal complexes: 2:D.195 MG.60: 5 residues within 4Å: Chain 3: D.9, Q.168, D.195, N.338 Ligands: ADP.59 1 PLIP interactions: 1 interactions with chain 3 Metal complexes: 3:D.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koh, F. et al., The structure of a 15-stranded actin-like filament from Clostridium botulinum. Nat Commun (2019)

Release Date

2019-06-19

Peptides

Putative plasmid segregation protein ParM: ABCDEFGHIJKLMNOPQRSTUVWXYZ0123

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
A

D
B

E
D

F
E

G
G

H
H

I
J

J
K

K
M

L
N

M
P

N
Q

O
b

P
c

Q
e

R
f

S
h

T
i

U
k

V
l

W
n

X
o

Y
q

Z
r

0
t

1
u

2
w

3
x

Putative plasmid segregation protein ParM

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