SMTL ID : 9p1i.1

Atomic structure of vibrio effector fragment VopV bound to Beta-cytoplasmic/gamma1-cytoplasmic F-actin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-12-12-mer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: Q.137, D.154, G.156 Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain B: Q.137, G.156 Ligands: ANP.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: Q.137, D.154 Ligands: ANP.6 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain D: Q.137, D.154, G.156 Ligands: ANP.8 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain E: D.154 Ligands: ANP.10 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain F: Q.137, D.154 Ligands: ANP.12 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain G: Q.137, G.156 Ligands: ANP.14 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain H: Q.137, G.156 Ligands: ANP.16 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain I: D.154, G.156 Ligands: ANP.18 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain J: Q.137, G.156 Ligands: ANP.20 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain K: Q.137, D.154, G.156 Ligands: ANP.22 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain L: Q.137, G.156 Ligands: ANP.24 No protein-ligand interaction detected (PLIP)

12 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 22 residues within 4Å: Chain A: G.13, S.14, G.15, M.16, K.18, Q.137, D.154, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.1 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.13, A:S.14, A:G.15, A:M.16, A:K.18, A:Q.137, A:Q.137, A:G.156, A:D.157, A:D.157, A:D.157, A:G.158, A:V.159, A:K.213, A:E.214, A:E.214, A:G.302, A:T.303, A:T.303, A:K.336 Salt bridges: A:K.18, A:K.336 pi-Stacking: A:Y.306 ANP.4: 21 residues within 4Å: Chain B: G.13, S.14, G.15, M.16, K.18, Q.137, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.3 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:S.14, B:G.15, B:M.16, B:Q.137, B:Q.137, B:G.156, B:D.157, B:D.157, B:D.157, B:G.158, B:V.159, B:K.213, B:E.214, B:E.214, B:G.302, B:T.303, B:K.336 Salt bridges: B:K.18, B:K.336 pi-Stacking: B:Y.306 ANP.6: 21 residues within 4Å: Chain C: G.13, S.14, G.15, M.16, K.18, Q.137, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.5 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:S.14, C:G.15, C:M.16, C:Q.137, C:G.156, C:D.157, C:D.157, C:D.157, C:G.158, C:V.159, C:K.213, C:E.214, C:E.214, C:G.302, C:T.303 Salt bridges: C:K.18, C:K.336 pi-Stacking: C:Y.306 ANP.8: 23 residues within 4Å: Chain D: D.11, G.13, S.14, G.15, M.16, K.18, Q.137, D.154, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.7 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:G.13, D:S.14, D:G.15, D:M.16, D:K.18, D:Q.137, D:Q.137, D:G.156, D:D.157, D:D.157, D:D.157, D:G.158, D:V.159, D:K.213, D:E.214, D:E.214, D:G.302, D:T.303 Salt bridges: D:K.18 pi-Stacking: D:Y.306 ANP.10: 21 residues within 4Å: Chain E: G.13, S.14, G.15, M.16, K.18, Q.137, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.9 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:S.14, E:G.15, E:M.16, E:Q.137, E:Q.137, E:G.156, E:D.157, E:D.157, E:D.157, E:G.158, E:V.159, E:K.213, E:E.214, E:E.214, E:G.302, E:T.303, E:T.303, E:K.336 Salt bridges: E:K.18 pi-Stacking: E:Y.306 ANP.12: 22 residues within 4Å: Chain F: G.13, S.14, G.15, M.16, K.18, Q.137, D.154, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.11 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:S.14, F:G.15, F:M.16, F:Q.137, F:Q.137, F:D.157, F:D.157, F:D.157, F:G.158, F:V.159, F:K.213, F:E.214, F:E.214, F:G.302, F:T.303 Salt bridges: F:K.18 pi-Stacking: F:Y.306 ANP.14: 21 residues within 4Å: Chain G: G.13, S.14, G.15, M.16, K.18, Q.137, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.13 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:S.14, G:G.15, G:M.16, G:Q.137, G:Q.137, G:G.156, G:D.157, G:G.158, G:V.159, G:K.213, G:E.214, G:E.214, G:G.302, G:T.303 Salt bridges: G:K.18, G:K.336 pi-Stacking: G:Y.306 ANP.16: 21 residues within 4Å: Chain H: G.13, S.14, G.15, M.16, K.18, Q.137, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.15 20 PLIP interactions: 20 interactions with chain H Hydrogen bonds: H:S.14, H:G.15, H:M.16, H:Q.137, H:Q.137, H:Q.137, H:G.156, H:D.157, H:D.157, H:D.157, H:G.158, H:V.159, H:K.213, H:E.214, H:G.302, H:T.303, H:K.336 Salt bridges: H:K.18, H:K.336 pi-Stacking: H:Y.306 ANP.18: 22 residues within 4Å: Chain I: G.13, S.14, G.15, M.16, K.18, Q.137, D.154, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.17 20 PLIP interactions: 20 interactions with chain I Hydrogen bonds: I:G.13, I:S.14, I:G.15, I:M.16, I:Q.137, I:G.156, I:D.157, I:D.157, I:D.157, I:G.158, I:V.159, I:K.213, I:E.214, I:E.214, I:G.302, I:T.303, I:K.336 Salt bridges: I:K.18, I:K.336 pi-Stacking: I:Y.306 ANP.20: 21 residues within 4Å: Chain J: G.13, S.14, G.15, M.16, K.18, G.74, Q.137, G.156, D.157, G.158, V.159, G.182, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.19 19 PLIP interactions: 19 interactions with chain J Hydrogen bonds: J:S.14, J:G.15, J:M.16, J:Q.137, J:Q.137, J:G.156, J:D.157, J:D.157, J:D.157, J:G.158, J:V.159, J:K.213, J:E.214, J:G.302, J:T.303, J:K.336 Salt bridges: J:K.18, J:K.336 pi-Stacking: J:Y.306 ANP.22: 21 residues within 4Å: Chain K: G.13, S.14, G.15, M.16, K.18, Q.137, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.21 21 PLIP interactions: 21 interactions with chain K Hydrogen bonds: K:G.13, K:S.14, K:G.15, K:M.16, K:K.18, K:Q.137, K:G.156, K:D.157, K:D.157, K:D.157, K:G.158, K:V.159, K:K.213, K:E.214, K:E.214, K:G.302, K:T.303, K:K.336 Salt bridges: K:K.18, K:K.336 pi-Stacking: K:Y.306 ANP.24: 21 residues within 4Å: Chain L: G.13, S.14, G.15, M.16, K.18, Q.137, G.156, D.157, G.158, V.159, G.182, R.210, K.213, E.214, G.301, G.302, T.303, M.305, Y.306, K.336 Ligands: MG.23 19 PLIP interactions: 19 interactions with chain L Hydrogen bonds: L:S.14, L:G.15, L:M.16, L:Q.137, L:Q.137, L:G.156, L:D.157, L:D.157, L:D.157, L:G.158, L:V.159, L:K.213, L:E.214, L:E.214, L:G.302, L:T.303 Salt bridges: L:K.18, L:K.336 pi-Stacking: L:Y.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kudryashova, E. et al., Actin isoform-specific interactions revealed by Vibrio VopV actin-binding repeat. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-11-19

Peptides

Actin, cytoplasmic 1: ABCDEFGHIJKL
VopV: MNOPQRSTUVWX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

B
R

C
S

D
T

E
U

F
V

G
W

H
X

I
Y

J
Z

K
a

L
b

M
c

N
d

O
e

P
f

Q
g

R
h

S
i

T
j

U
k

V
l

W
m

X
n

Actin, cytoplasmic 1

VopV

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