SMTL ID : 6fkf.1

Chloroplast F1Fo conformation 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.15 Å

Oligo State

hetero-3-3-1-1-1-1-1-14-1-mer

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: R.172, Q.173, T.174, G.175, K.176, T.177, A.178, F.350, R.355, P.356, Q.423, P.424, Q.425 Chain F: T.373, Q.376, Y.385 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Q.173, A:Q.173, A:T.174, A:G.175, A:K.176, A:T.177, A:T.177, A:A.178, A:R.355, A:Q.423, A:Q.425 Water bridges: A:K.176, A:K.176, A:T.177 Salt bridges: A:K.176, A:K.176 pi-Stacking: A:F.350 ATP.3: 14 residues within 4Å: Chain B: R.378 Chain C: R.172, Q.173, T.174, G.175, K.176, T.177, A.178, F.350, R.355, Q.423, P.424, Q.425 Ligands: MG.4 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.173, C:T.174, C:G.175, C:K.176, C:T.177, C:A.178, C:Q.423, C:Q.425, C:Q.425, B:R.378 Water bridges: C:Q.201, C:K.202, C:K.202, C:S.205 Salt bridges: C:K.176, C:K.176 ATP.7: 17 residues within 4Å: Chain D: T.373, Q.376, Y.385 Chain E: D.171, R.172, Q.173, T.174, G.175, K.176, T.177, A.178, F.350, R.355, P.356, Q.423, Q.425 Ligands: MG.8 18 PLIP interactions: 15 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:Q.173, E:Q.173, E:T.174, E:G.175, E:K.176, E:T.177, E:T.177, E:A.178, E:Q.423, D:T.373, D:Q.376, D:Y.385 Water bridges: E:K.176, E:K.176, E:T.177, E:S.205 Salt bridges: E:K.176, E:K.176

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.177, D.262 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.177, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain C: T.177, D.262 Ligands: ATP.3 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.177, H2O.1 MG.6: 3 residues within 4Å: Chain D: T.179, R.205 Ligands: ADP.5 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.179, H2O.1, H2O.1 MG.8: 2 residues within 4Å: Chain E: T.177 Ligands: ATP.7 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:T.177, H2O.1 MG.10: 4 residues within 4Å: Chain F: T.179, E.204, D.273 Ligands: ADP.9 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.179, H2O.1, H2O.1

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

ADP.5: 13 residues within 4Å: Chain C: R.366 Chain D: G.173, G.175, V.176, G.177, K.178, T.179, V.180, Y.362, F.435, A.438, F.441 Ligands: MG.6 13 PLIP interactions: 1 interactions with chain C, 12 interactions with chain D Water bridges: C:D.340, D:E.204, D:R.205 Hydrogen bonds: D:G.175, D:V.176, D:G.177, D:K.178, D:T.179, D:T.179, D:V.180 Salt bridges: D:K.178 pi-Stacking: D:Y.362, D:Y.362 ADP.9: 17 residues within 4Å: Chain E: V.364, S.365, R.366 Chain F: G.173, A.174, G.175, V.176, G.177, K.178, T.179, V.180, Y.362, F.435, A.438, F.441, T.442 Ligands: MG.10 20 PLIP interactions: 16 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:G.175, F:V.176, F:G.177, F:K.178, F:T.179, F:T.179, F:V.180, E:S.365 Water bridges: F:K.178, F:T.179, F:R.205, F:R.205, F:R.205, F:R.205, E:R.366 Salt bridges: F:K.178, E:R.366, E:R.366 pi-Stacking: F:Y.362, F:Y.362

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hahn, A. et al., Structure, mechanism, and regulation of the chloroplast ATP synthase. Science (2018)

Release Date

2018-05-23

Peptides

ATP synthase subunit alpha, chloroplastic: ACE
ATP synthase subunit beta, chloroplastic: BDF
ATP synthase gamma chain, chloroplastic: G
ATP synthase delta chain, chloroplastic: H
ATP synthase subunit b', chloroplastic: I
ATP synthase subunit b, chloroplastic: J
ATP synthase subunit a, chloroplastic: K
ATP synthase subunit c, chloroplastic: LMNOPQRSTUVWXY
ATP synthase epsilon chain, chloroplastic: Z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
g

H
d

I
p

J
b

K
a

L
S

M
N

N
O

O
P

P
Q

Q
R

R
M

S
T

T
G

U
H

V
L

W
K

X
J

Y
I

Z
e

Membrane

We predict this structure to be a membrane protein.
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ATP synthase subunit alpha, chloroplastic

ATP synthase subunit beta, chloroplastic

ATP synthase gamma chain, chloroplastic

ATP synthase delta chain, chloroplastic

ATP synthase subunit b', chloroplastic

ATP synthase subunit b, chloroplastic

ATP synthase subunit a, chloroplastic

ATP synthase subunit c, chloroplastic

ATP synthase epsilon chain, chloroplastic

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