SMTL ID : 8vaa.1

Actin-binding domain of Legionella pneumophila effector LFAT1 (lpg1387) bound to F-actin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-10-mer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: G.9, S.10, G.11, L.12, K.14, Q.133, G.152, D.153, G.178, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.10, A:G.11, A:L.12, A:D.153, A:K.209, A:G.298 Salt bridges: A:K.14, A:K.14 pi-Stacking: A:Y.302 ADP.3: 18 residues within 4Å: Chain B: G.9, S.10, G.11, L.12, K.14, Q.133, G.152, D.153, G.178, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.10, B:G.11, B:L.12, B:D.153, B:K.209, B:G.298 Salt bridges: B:K.14, B:K.14 pi-Stacking: B:Y.302 ADP.5: 18 residues within 4Å: Chain C: G.9, S.10, G.11, L.12, K.14, Q.133, G.152, D.153, G.178, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.6 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.10, C:G.11, C:L.12, C:D.153, C:K.209, C:G.298 Salt bridges: C:K.14, C:K.14 pi-Stacking: C:Y.302 ADP.7: 18 residues within 4Å: Chain D: G.9, S.10, G.11, L.12, K.14, Q.133, G.152, D.153, G.178, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.10, D:G.11, D:L.12, D:D.153, D:K.209, D:G.298 Salt bridges: D:K.14, D:K.14 pi-Stacking: D:Y.302 ADP.9: 19 residues within 4Å: Chain E: G.9, S.10, G.11, L.12, K.14, Q.133, G.152, D.153, G.178, T.182, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.10 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.10, E:G.11, E:L.12, E:D.153, E:D.153, E:K.209, E:G.298 Salt bridges: E:K.14, E:K.14 pi-Stacking: E:Y.302 ADP.11: 18 residues within 4Å: Chain F: G.9, S.10, G.11, L.12, K.14, G.152, D.153, G.178, T.182, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:S.10, F:G.11, F:L.12, F:D.153, F:K.209, F:G.298 Salt bridges: F:K.14, F:K.14 ADP.13: 18 residues within 4Å: Chain G: G.9, S.10, G.11, L.12, K.14, G.152, D.153, G.178, T.182, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.14 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:S.10, G:G.11, G:L.12, G:D.153, G:K.209, G:G.298 Salt bridges: G:K.14, G:K.14 ADP.15: 18 residues within 4Å: Chain H: G.9, S.10, G.11, L.12, K.14, G.152, D.153, G.178, T.182, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.16 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:S.10, H:G.11, H:L.12, H:D.153, H:K.209, H:G.298 Salt bridges: H:K.14, H:K.14 pi-Stacking: H:Y.302 ADP.17: 17 residues within 4Å: Chain I: G.9, S.10, G.11, L.12, K.14, G.152, D.153, G.178, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.18 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:D.7, I:S.10, I:G.11, I:L.12, I:D.153, I:K.209, I:G.298 Salt bridges: I:K.14, I:K.14 pi-Stacking: I:Y.302 ADP.19: 17 residues within 4Å: Chain J: G.9, S.10, G.11, L.12, K.14, G.152, D.153, G.178, R.206, K.209, E.210, G.298, T.299, M.301, Y.302, K.332 Ligands: MG.20 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:S.10, J:G.11, J:L.12, J:D.153, J:K.209, J:G.298 Salt bridges: J:K.14, J:K.14 pi-Stacking: J:Y.302

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

MG.2: 4 residues within 4Å: Chain A: K.14, G.152, G.297 Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: K.14, G.152, G.297 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain C: K.14, G.152, G.297 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain D: K.14, G.152, G.297, V.335 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 6 residues within 4Å: Chain E: K.14, Q.133, G.152, G.297, V.335 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain F: K.14, G.152, G.297, V.335 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain G: K.14, G.152, G.297 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain H: K.14, G.152, G.297 Ligands: ADP.15 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain I: K.14, G.152, G.297 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain J: K.14, G.152, G.297 Ligands: ADP.19 No protein-ligand interaction detected (PLIP)

Links

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Citation

Zeng, W. et al., Structural basis for a novel F-actin binding domain from the Legionella pneumophila lysine fatty-acyltransferase LFAT1. To Be Published

Release Date

2024-12-18

Peptides

Actin, alpha skeletal muscle: ABCDEFGHIJ
F-actin-binding Coiled-Coil domain of LFAT1: KLMNOPQRST

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
S

T
T

Actin, alpha skeletal muscle

F-actin-binding Coiled-Coil domain of LFAT1