SMTL ID : 6wnr.1

E. coli ATP synthase State 3b

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-2-1-1-3-10-1-mer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain B: R.171, Q.172, T.173, G.174, K.175, T.176, A.177, E.331, F.360, R.365, P.366, Q.433, Q.435 Chain I: R.354, D.357 Ligands: MG.2 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain I Hydrogen bonds: B:Q.172, B:T.173, B:T.173, B:G.174, B:K.175, B:T.176, B:T.176, B:A.177, B:E.331, B:E.331, B:R.365, B:Q.433, B:Q.435 Salt bridges: B:K.175, B:K.175, I:R.354, I:R.354 ATP.3: 13 residues within 4Å: Chain C: R.171, Q.172, T.173, G.174, K.175, T.176, A.177, F.360, R.365, Q.433, Q.435 Chain J: R.354 Ligands: MG.4 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain J Hydrogen bonds: C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:A.177, C:R.365, C:Q.433, C:Q.435 Salt bridges: C:K.175, C:K.175, J:R.354, J:R.354, J:R.354 pi-Stacking: C:F.360 ATP.5: 17 residues within 4Å: Chain D: Y.150, R.171, Q.172, T.173, G.174, K.175, T.176, A.177, F.360, R.365, P.366, Q.433, Q.435 Chain H: R.354, D.357, Y.366 Ligands: MG.6 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain H Hydrogen bonds: D:Q.172, D:T.173, D:G.174, D:K.175, D:T.176, D:A.177, D:Q.433, D:Q.435, H:D.357, H:Y.366 Salt bridges: D:K.175, D:K.175, H:R.354

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: T.176 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain C: T.176 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.176 MG.6: 2 residues within 4Å: Chain D: T.176 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.176 MG.8: 5 residues within 4Å: Chain B: R.376 Chain H: K.167, T.168, R.194 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain J: T.168, R.194 Ligands: ADP.10, PO4.11 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.168

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

ADP.7: 13 residues within 4Å: Chain B: V.374, R.376 Chain H: G.164, V.165, G.166, K.167, T.168, V.169, Y.343, F.416, A.419, F.422 Ligands: MG.8 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain B Hydrogen bonds: H:G.164, H:V.165, H:G.166, H:K.167, H:T.168, H:T.168, H:V.169 Salt bridges: H:K.167, B:R.376, B:R.376 pi-Stacking: H:Y.343, H:Y.343 ADP.9: 12 residues within 4Å: Chain I: A.163, G.164, V.165, G.166, K.167, T.168, V.169, Y.343, F.416, A.419, F.422, T.423 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:G.164, I:V.165, I:G.166, I:K.167, I:T.168 pi-Stacking: I:Y.343 ADP.10: 15 residues within 4Å: Chain D: R.376 Chain J: A.163, G.164, V.165, G.166, K.167, T.168, V.169, E.197, Y.343, F.416, A.419, F.422 Ligands: PO4.11, MG.12 13 PLIP interactions: 11 interactions with chain J, 2 interactions with chain D Hydrogen bonds: J:G.164, J:V.165, J:G.166, J:K.167, J:T.168, J:T.168, J:T.168, J:V.169, D:R.376 Salt bridges: J:K.167, D:R.376 pi-Stacking: J:Y.343, J:Y.343

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

PO4.11: 9 residues within 4Å: Chain D: R.376 Chain J: G.162, A.163, K.167, R.194, N.255, R.258 Ligands: ADP.10, MG.12 6 PLIP interactions: 5 interactions with chain J, 1 interactions with chain D Hydrogen bonds: J:G.162, J:N.255 Salt bridges: J:K.167, J:R.194, J:R.258, D:R.376

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sobti, M. et al., Cryo-EM structures provide insight into how E. coli F1FoATP synthase accommodates symmetry mismatch. Nat Commun (2020)

Release Date

2020-06-03

Peptides

ATP synthase subunit delta: A
ATP synthase subunit alpha: BCD
ATP synthase subunit b: EU
ATP synthase epsilon chain: F
ATP synthase gamma chain: G
ATP synthase subunit beta: HIJ
ATP synthase subunit c: KLMNOPQRST
ATP synthase subunit a: V

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
W

B
C

C
B

D
A

E
X

U
Y

F
H

G
G

H
F

I
E

J
D

K
I

L
J

M
L

N
M

O
N

P
O

Q
P

R
Q

S
R

T
S

V
a

Membrane

We predict this structure to be a membrane protein.
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ATP synthase subunit delta

ATP synthase subunit alpha

ATP synthase subunit b

ATP synthase epsilon chain

ATP synthase gamma chain

ATP synthase subunit beta

ATP synthase subunit c

ATP synthase subunit a

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