SMTL ID : 5dn6.1

ATP synthase from Paracoccus denitrificans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.98 Å

Oligo State

hetero-1-1-1-3-3-1-1-1-12-1-1-1-1-1-mer

Ligands

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

ATP.1: 13 residues within 4Å: Chain D: R.171, G.174, K.175, T.176, A.177, E.329, F.358, P.364, Q.431, Q.433 Chain G: S.351, Y.364 Ligands: MG.2 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain G Hydrogen bonds: D:G.174, D:K.175, D:T.176, D:A.177, D:E.329, D:Q.431, G:S.351 Salt bridges: D:K.175, D:K.175 pi-Stacking: D:F.358 ATP.5: 15 residues within 4Å: Chain F: R.171, Q.172, T.173, G.174, K.175, T.176, A.177, E.329, F.358, R.363, P.364, Q.431, Q.433 Chain I: Y.364 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Q.172, F:Q.172, F:T.173, F:G.174, F:K.175, F:T.176, F:A.177, F:R.363, F:Q.431, F:Q.433 Salt bridges: F:K.175, F:K.175 pi-Stacking: F:F.358 pi-Cation interactions: F:R.363 ATP.7: 17 residues within 4Å: Chain F: V.372, S.373, R.374 Chain G: G.152, G.154, V.155, G.156, K.157, T.158, V.159, R.184, E.187, Y.341, F.414, A.417, F.420 Ligands: MG.8 13 PLIP interactions: 11 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:G.154, G:V.155, G:G.156, G:K.157, G:T.158, G:V.159 Salt bridges: G:K.157, G:K.157, G:R.184, F:R.374, F:R.374 pi-Stacking: G:Y.341, G:Y.341 ATP.9: 19 residues within 4Å: Chain E: S.345, V.372, R.374 Chain I: G.152, G.154, V.155, G.156, K.157, T.158, V.159, E.183, R.184, D.252, Y.341, F.414, A.417, F.420, T.421 Ligands: MG.10 15 PLIP interactions: 13 interactions with chain I, 2 interactions with chain E Hydrogen bonds: I:G.154, I:V.155, I:G.156, I:K.157, I:T.158, I:T.158, I:V.159, I:E.183, E:R.374 Salt bridges: I:K.157, I:K.157, I:R.184, E:R.374 pi-Stacking: I:Y.341, I:Y.341

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain D: T.176 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.176 MG.4: 4 residues within 4Å: Chain E: T.176, Q.209, D.270 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.176 MG.6: 3 residues within 4Å: Chain F: T.176, D.270 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.176 MG.8: 6 residues within 4Å: Chain G: T.158, E.183, R.184, E.187, D.252 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.158 MG.10: 5 residues within 4Å: Chain I: T.158, E.183, E.187, D.252 Ligands: ATP.9 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:T.158, I:D.252

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

ADP.3: 15 residues within 4Å: Chain E: Q.172, T.173, G.174, K.175, T.176, A.177, F.358, R.363, P.364, Q.431, P.432, Q.433 Chain H: R.352, D.355 Ligands: MG.4 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:D.170, E:Q.172, E:T.173, E:G.174, E:K.175, E:T.176, E:A.177, E:R.363, E:Q.431, H:D.355 Salt bridges: E:K.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morales-Rios, E. et al., Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 angstrom resolution. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-10-28

Peptides

Chain A: A
Chain B: B
Chain C: C
ATP synthase subunit alpha: DEF
ATP synthase subunit beta: GHI
ATP synthase gamma chain: J
ATP synthase subunit delta: K
ATP synthase epsilon chain: L
ATP synthase F0 subcomplex C subunit: MNOPQRSTUVWX
Chain V: Y
Chain W: Z
ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a: 0
Chain Y: 1
Zeta inhibitor protein: 2

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
A

E
B

F
C

G
D

H
E

I
F

J
G

K
H

L
I

M
J

N
K

O
L

P
M

Q
N

R
O

S
P

T
Q

U
R

V
S

W
T

X
U

Y
V

Z
W

0
X

1
Y

2
Z

Membrane

We predict this structure to be a membrane protein.
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Chain A

Chain B

Chain C

ATP synthase subunit alpha

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase subunit delta

ATP synthase epsilon chain

ATP synthase F0 subcomplex C subunit

Chain V

Chain W

ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a,ATP synthase subunit a

Chain Y

Zeta inhibitor protein

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