SMTL ID : 8c4c.1

F-actin decorated by SipA497-669

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-4-mer

Ligands

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

ADP.1: 21 residues within 4Å: Chain A: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, T.188, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: PO4.2, MG.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.16, A:S.16, A:S.16, A:G.17, A:L.18, A:L.18, A:D.159, A:K.215, A:E.216, A:E.216, A:G.304, A:T.305, A:M.307, A:K.338 Salt bridges: A:K.20, A:K.20 pi-Stacking: A:Y.308 ADP.5: 20 residues within 4Å: Chain B: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: PO4.4, MG.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.16, B:G.17, B:L.18, B:L.18, B:D.159, B:K.215, B:E.216, B:E.216, B:G.304, B:K.338 Salt bridges: B:K.20, B:K.20 pi-Stacking: B:Y.308 ADP.7: 21 residues within 4Å: Chain C: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, T.188, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.8, PO4.9 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:S.16, C:G.17, C:L.18, C:L.18, C:D.159, C:K.215, C:E.216, C:E.216, C:G.304, C:T.305, C:K.338 Salt bridges: C:K.20, C:K.20 pi-Stacking: C:Y.308 ADP.11: 20 residues within 4Å: Chain D: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.10, PO4.12 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:S.16, D:G.17, D:L.18, D:L.18, D:D.159, D:K.215, D:E.216, D:G.304, D:T.305, D:K.338 Salt bridges: D:K.20, D:K.20 pi-Stacking: D:Y.308 ADP.14: 21 residues within 4Å: Chain E: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, T.188, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.13, PO4.15 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:S.16, E:G.17, E:L.18, E:L.18, E:D.159, E:K.215, E:G.304, E:K.338 Salt bridges: E:K.20, E:K.20 pi-Stacking: E:Y.308 ADP.17: 20 residues within 4Å: Chain F: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.16, PO4.18 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:S.16, F:G.17, F:L.18, F:L.18, F:D.159, F:G.160, F:K.215, F:E.216, F:G.304, F:K.338 Salt bridges: F:K.20, F:K.20 pi-Stacking: F:Y.308 ADP.20: 21 residues within 4Å: Chain G: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, T.188, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: PO4.19, MG.21 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:S.16, G:G.17, G:L.18, G:L.18, G:D.159, G:K.215, G:E.216, G:G.304, G:K.338 Salt bridges: G:K.20, G:K.20 pi-Stacking: G:Y.308 ADP.24: 21 residues within 4Å: Chain H: G.15, S.16, G.17, L.18, K.20, G.158, D.159, G.160, G.184, T.188, R.212, K.215, E.216, G.303, G.304, T.305, M.307, Y.308, K.338 Ligands: MG.22, PO4.23 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:S.16, H:G.17, H:L.18, H:L.18, H:D.159, H:D.159, H:G.160, H:K.215, H:E.216, H:G.304, H:T.305, H:K.338 Salt bridges: H:K.20, H:K.20 pi-Stacking: H:Y.308

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 13 residues within 4Å: Chain A: G.15, S.16, G.76, A.110, Q.139, D.156, G.158, D.159, G.160, V.161, H.163 Ligands: ADP.1, MG.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.16, A:Q.139, A:Q.139, A:D.156, A:G.158, A:D.159, A:G.160, A:V.161 PO4.4: 12 residues within 4Å: Chain B: G.15, S.16, G.76, A.110, Q.139, G.158, D.159, G.160, V.161, H.163 Ligands: ADP.5, MG.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.16, B:S.16, B:Q.139, B:Q.139, B:G.158, B:D.159, B:G.160, B:V.161, B:V.161 PO4.9: 12 residues within 4Å: Chain C: G.15, S.16, G.76, A.110, Q.139, G.158, D.159, G.160, V.161, H.163 Ligands: ADP.7, MG.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:S.16, C:S.16, C:Q.139, C:Q.139, C:G.158, C:D.159, C:G.160, C:V.161 PO4.12: 12 residues within 4Å: Chain D: G.15, S.16, G.76, A.110, Q.139, G.158, D.159, G.160, V.161, H.163 Ligands: MG.10, ADP.11 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.16, D:S.16, D:Q.139, D:Q.139, D:D.156, D:G.158, D:D.159, D:G.160, D:V.161 PO4.15: 12 residues within 4Å: Chain E: G.15, S.16, G.76, A.110, Q.139, G.158, D.159, G.160, V.161, H.163 Ligands: MG.13, ADP.14 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:S.16, E:S.16, E:Q.139, E:Q.139, E:G.158, E:D.159, E:G.160, E:V.161 PO4.18: 12 residues within 4Å: Chain F: G.15, S.16, G.76, A.110, Q.139, G.158, D.159, G.160, V.161, H.163 Ligands: MG.16, ADP.17 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:S.16, F:S.16, F:Q.139, F:Q.139, F:G.158, F:D.159, F:G.160, F:V.161 PO4.19: 13 residues within 4Å: Chain G: G.15, S.16, G.76, A.110, Q.139, D.156, G.158, D.159, G.160, V.161, H.163 Ligands: ADP.20, MG.21 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:S.16, G:S.16, G:Q.139, G:Q.139, G:D.156, G:D.159, G:G.160, G:V.161, G:H.163 PO4.23: 12 residues within 4Å: Chain H: G.15, S.16, G.76, A.110, Q.139, G.158, D.159, G.160, V.161, H.163 Ligands: MG.22, ADP.24 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:S.16, H:Q.139, H:Q.139, H:G.158, H:D.159, H:G.160, H:V.161, H:V.161

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 7 residues within 4Å: Chain A: K.20, D.156, G.158, G.303, V.341 Ligands: ADP.1, PO4.2 No protein-ligand interaction detected (PLIP) MG.6: 6 residues within 4Å: Chain B: D.13, G.15, K.20, G.158 Ligands: PO4.4, ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain C: K.20, G.158, V.341 Ligands: ADP.7, PO4.9 No protein-ligand interaction detected (PLIP) MG.10: 7 residues within 4Å: Chain D: K.20, D.156, G.158, G.303, V.341 Ligands: ADP.11, PO4.12 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain E: K.20, G.158, G.303 Ligands: ADP.14, PO4.15 No protein-ligand interaction detected (PLIP) MG.16: 6 residues within 4Å: Chain F: K.20, D.156, G.158, V.341 Ligands: ADP.17, PO4.18 No protein-ligand interaction detected (PLIP) MG.21: 6 residues within 4Å: Chain G: K.20, D.156, G.158, V.341 Ligands: PO4.19, ADP.20 No protein-ligand interaction detected (PLIP) MG.22: 5 residues within 4Å: Chain H: K.20, G.158, G.303 Ligands: PO4.23, ADP.24 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, B. et al., Structural basis for subversion of host cell actin cytoskeleton during Salmonella infection. Sci Adv (2023)

Release Date

2024-01-17

Peptides

Actin, alpha skeletal muscle: ABCDEFGH
Cell invasion protein SipA: IJKL

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
K

J
L

K
M

L
N

Actin, alpha skeletal muscle

Cell invasion protein SipA

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