SMTL ID : 6n2y.1

Bacillus PS3 ATP synthase class 1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

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

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: D.170, R.171, Q.172, T.173, G.174, K.175, T.176, S.177, Q.200, F.349, R.354, P.355, Q.422, L.424 Chain D: R.352, A.355 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.172, A:T.173, A:G.174, A:K.175, A:T.176, A:T.176, A:S.177, A:S.177, A:Q.200, A:Q.422 Salt bridges: A:K.175, A:K.175 ATP.3: 14 residues within 4Å: Chain B: Q.172, T.173, G.174, K.175, T.176, S.177, Q.200, F.349, R.354, P.355, Q.422, D.423, L.424 Ligands: MG.4 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.172, B:Q.172, B:T.173, B:G.174, B:K.175, B:T.176, B:S.177, B:S.177, B:Q.200, B:R.354, B:Q.422, B:L.424 Salt bridges: B:K.175, B:K.175 ATP.5: 16 residues within 4Å: Chain C: R.171, Q.172, T.173, G.174, K.175, T.176, S.177, F.349, R.354, P.355, Q.422, D.423, L.424 Chain F: R.352, Y.364 Ligands: MG.6 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:Q.172, C:Q.172, C:T.173, C:G.174, C:K.175, C:T.176, C:S.177, C:S.177, C:Q.422 Salt bridges: C:K.175, C:K.175, F:R.352, F:R.352, F:R.352

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.176, Q.200, D.261 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.176 MG.4: 4 residues within 4Å: Chain B: T.176, Q.200, D.261 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.176 MG.6: 3 residues within 4Å: Chain C: T.176, D.261 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.176 MG.9: 3 residues within 4Å: Chain F: T.165, R.191 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.165

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

PO4.7: 7 residues within 4Å: Chain E: G.159, A.160, G.161, V.162, G.163, K.164, T.165 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.161, E:V.162, E:G.163, E:K.164, E:T.165

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

ADP.8: 13 residues within 4Å: Chain B: V.363, R.365 Chain F: G.161, V.162, G.163, K.164, T.165, V.166, Y.341, F.414, A.417, F.420 Ligands: MG.9 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:G.161, F:V.162, F:G.163, F:K.164, F:T.165, F:V.166, B:R.365 Salt bridges: F:K.164, B:R.365, B:R.365 pi-Stacking: F:Y.341, F:Y.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, H. et al., Structure of a bacterial ATP synthase. Elife (2019)

Release Date

2019-02-20

Peptides

ATP synthase subunit alpha: ABC
ATP synthase subunit beta: DEF
ATP synthase gamma chain: G
ATP synthase epsilon chain: H
ATP synthase subunit delta: I
ATP synthase subunit b: J
ATP synthase subunit b: K
ATP synthase subunit a: L
ATP synthase subunit c: MNOPQRSTUV

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
b2

K
b1

L
a

M
c0

N
c1

O
c2

P
c3

Q
c4

R
c5

S
c6

T
c7

U
c8

V
c9

Membrane

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

ATP synthase subunit beta

ATP synthase gamma chain

ATP synthase epsilon chain

ATP synthase subunit delta

ATP synthase subunit b

ATP synthase subunit b

ATP synthase subunit a

ATP synthase subunit c

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