SMTL ID : 8dbw.1

E. coli ATP synthase imaged in 10mM MgATP State3 "down" Fo classified

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: Y.149, D.169, R.170, Q.171, T.172, G.173, K.174, T.175, A.176, F.359, R.364, Q.432, Q.434 Chain F: S.342, R.343, D.346, Y.355 Ligands: MG.2 15 PLIP interactions: 4 interactions with chain F, 11 interactions with chain A Hydrogen bonds: F:S.342, F:D.346, F:Y.355, A:Q.171, A:T.172, A:G.173, A:K.174, A:T.175, A:A.176, A:R.364, A:Q.432, A:Q.434 Salt bridges: F:R.343, A:K.174, A:K.174 ATP.3: 16 residues within 4Å: Chain B: D.169, R.170, Q.171, T.172, G.173, K.174, T.175, A.176, F.359, R.364, Q.432, Q.434 Chain D: R.343, D.346, Y.355 Ligands: MG.4 13 PLIP interactions: 2 interactions with chain D, 11 interactions with chain B Salt bridges: D:R.343, D:R.343, B:K.174, B:K.174 Hydrogen bonds: B:Q.171, B:T.172, B:G.173, B:K.174, B:T.175, B:A.176, B:R.364, B:Q.432, B:Q.434 ATP.5: 16 residues within 4Å: Chain C: D.169, R.170, Q.171, T.172, G.173, K.174, T.175, A.176, F.359, R.364, Q.432, K.433, Q.434 Chain E: R.343, D.346 Ligands: MG.6 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:Q.171, C:T.172, C:G.173, C:K.174, C:T.175, C:T.175, C:A.176, C:R.364, C:Q.432, C:Q.434, C:Q.434, E:R.343 Salt bridges: C:K.174, C:K.174, E:R.343 ATP.11: 14 residues within 4Å: Chain C: S.346, R.375 Chain F: G.151, G.153, V.154, G.155, K.156, T.157, V.158, R.183, Y.332, A.408, F.411 Ligands: MG.10 16 PLIP interactions: 12 interactions with chain F, 4 interactions with chain C Hydrogen bonds: F:G.153, F:V.154, F:G.155, F:K.156, F:T.157, F:T.157, F:V.158, C:R.375 Salt bridges: F:K.156, F:K.156, F:R.183, C:R.375, C:R.375, C:R.375 pi-Stacking: F:Y.332, F:Y.332

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.175 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.175 MG.4: 3 residues within 4Å: Chain B: T.175 Chain D: R.343 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.175 MG.6: 3 residues within 4Å: Chain C: T.175, Q.199 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.175 MG.8: 2 residues within 4Å: Chain D: T.157 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.157 MG.10: 2 residues within 4Å: Chain F: T.157 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.157

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

ADP.7: 13 residues within 4Å: Chain A: S.374, R.375 Chain D: G.153, V.154, G.155, K.156, T.157, V.158, Y.332, F.405, A.408, F.411 Ligands: MG.8 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:G.153, D:V.154, D:G.155, D:K.156, D:T.157, D:V.158, A:S.374 pi-Stacking: D:Y.332, D:Y.332 Salt bridges: A:R.375, A:R.375 ADP.9: 8 residues within 4Å: Chain E: G.153, V.154, G.155, T.157, V.158, Y.332, A.408, F.411 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:K.156, E:T.157, E:T.157 pi-Stacking: E:Y.332, E:Y.332

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sobti, M. et al., Changes within the central stalk of E. coli F 1 F o ATP synthase observed after addition of ATP. Commun Biol (2023)

Release Date

2023-01-25

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H
ATP synthase subunit c: IJKLMNOPQR
ATP synthase subunit delta: S
ATP synthase subunit b: TU
ATP synthase subunit a: V

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
L

L
M

M
N

N
O

O
P

P
Q

Q
R

R
S

S
W

T
X

U
Y

V
a

Membrane

We predict this structure to be a membrane protein.
Show / Hide

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

ATP synthase subunit c

ATP synthase subunit delta

ATP synthase subunit b

ATP synthase subunit a

Related Entries With Identical Sequence