SMTL ID : 7ajf.1

bovine ATP synthase dimer state2:state2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-2-2-2-2-16-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.1: 15 residues within 4Å: Chain 0: L.5, I.6, V.9, W.10 Chain T: L.22, I.23, F.26, L.29, F.31, P.32 Chain X: F.37, Q.38, Y.41 Ligands: CDL.3, LHG.5 8 PLIP interactions: 4 interactions with chain 0, 2 interactions with chain T, 2 interactions with chain X Hydrophobic interactions: 0:L.5, 0:I.6, 0:V.9, 0:W.10, T:F.26, X:F.37, X:Y.41 Hydrogen bonds: T:F.31 CDL.2: 17 residues within 4Å: Chain T: R.41, F.42, L.45, M.49 Chain U: F.14, I.64, L.67, V.68, V.71, K.72, G.75, A.76, G.79 Chain X: K.52, K.53, I.56, L.59 8 PLIP interactions: 5 interactions with chain U, 1 interactions with chain T, 2 interactions with chain X Hydrophobic interactions: U:I.64, U:L.67, U:V.68, U:V.71, T:R.41, X:I.56, X:L.59 Hydrogen bonds: U:V.68 CDL.3: 15 residues within 4Å: Chain U: P.18, E.19, E.20, F.21 Chain X: R.43, Y.44, K.47, Y.48, V.49, G.58, S.60, M.61, A.64 Ligands: CDL.1, LHG.5 10 PLIP interactions: 8 interactions with chain X, 2 interactions with chain U Hydrophobic interactions: X:Y.48, X:V.49, X:S.60, X:M.61, X:A.64, X:A.64, U:P.18 Hydrogen bonds: X:K.47, X:Y.48, U:F.21 CDL.6: 21 residues within 4Å: Ligands: CDL.8, LHG.10 Chain l: L.22, I.23, L.25, F.26, S.28, L.29, F.31, P.32, T.33 Chain p: I.33, A.34, G.35, F.37, Q.38, Y.41 Chain s: L.5, I.6, V.9, W.10 18 PLIP interactions: 7 interactions with chain p, 8 interactions with chain l, 3 interactions with chain s Hydrophobic interactions: p:I.33, p:F.37, p:F.37, p:F.37, p:Q.38, p:Y.41, l:L.22, l:I.23, l:L.25, l:F.26, l:S.28, l:L.29, s:L.5, s:V.9, s:W.10 Hydrogen bonds: p:Q.38, l:T.33, l:T.33 CDL.7: 20 residues within 4Å: Chain l: F.42, L.45, Q.46, M.49 Chain m: F.14, T.63, F.66, L.67, V.68, V.71, K.72, G.75, A.76, V.78, G.79 Chain p: K.52, K.53, G.54, I.56, S.60 8 PLIP interactions: 4 interactions with chain m, 2 interactions with chain l, 2 interactions with chain p Hydrophobic interactions: m:F.14, m:F.66, m:L.67, l:L.45, l:Q.46, p:S.60 Hydrogen bonds: m:V.68, p:G.54 CDL.8: 20 residues within 4Å: Ligands: CDL.6, LHG.10 Chain l: L.29 Chain m: L.16, I.17, P.18, E.20, F.21, Q.23, F.24, L.25 Chain p: G.40, R.43, Y.44, K.47, Y.48, A.57, G.58, M.61, A.64 11 PLIP interactions: 3 interactions with chain p, 8 interactions with chain m Hydrophobic interactions: p:R.43, p:M.61, p:A.64, m:P.18, m:F.21, m:F.24, m:L.25 Hydrogen bonds: m:P.18, m:F.21, m:Q.23, m:F.24

4 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Non-covalent)(Non-functional Binders)

LHG.4: 12 residues within 4Å: Chain U: L.41, L.45, I.50, Y.51, V.52, I.53 Chain X: F.68, Y.71, C.72, Y.75, L.78, K.79 7 PLIP interactions: 3 interactions with chain X, 4 interactions with chain U Hydrophobic interactions: X:Y.71, X:L.78, X:K.79, U:L.41, U:Y.51, U:V.52, U:I.53 LHG.5: 2 residues within 4Å: Ligands: CDL.1, CDL.3 No protein-ligand interaction detected (PLIP) LHG.9: 12 residues within 4Å: Chain l: H.90 Chain m: L.37, G.38, L.41, K.48, I.50, Y.51 Chain p: V.67, F.68, Y.71, C.72, Y.75 9 PLIP interactions: 3 interactions with chain m, 1 interactions with chain l, 5 interactions with chain p Hydrophobic interactions: m:L.41, m:I.50, l:H.90, p:V.67, p:F.68, p:Y.71, p:Y.75, p:Y.75 Hydrogen bonds: m:K.48 LHG.10: 6 residues within 4Å: Ligands: CDL.6, CDL.8 Chain p: K.10, L.11, L.12, A.36 3 PLIP interactions: 3 interactions with chain p Hydrogen bonds: p:K.10, p:L.11, p:L.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spikes, T.E. et al., Interface mobility between monomers in dimeric bovine ATP synthase participates in the ultrastructure of inner mitochondrial membranes. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-02-03

Peptides

ATP synthase subunit alpha, mitochondrial: ABC234
ATP synthase subunit beta, mitochondrial: DEF567
ATP synthase subunit gamma, mitochondrial: G8
ATP synthase subunit delta, mitochondrial: H9
ATP synthase subunit epsilon, mitochondrial: Ia
ATPase inhibitor, mitochondrial: Jb
ATP synthase F(0) complex subunit C2, mitochondrial: KLMNOPQRcdefghij
ATP synthase subunit O, mitochondrial: Sk
ATP synthase subunit a: Tl
ATP synthase F(0) complex subunit B1, mitochondrial: Um
ATP synthase subunit d, mitochondrial: Vn
ATP synthase subunit e, mitochondrial: Wo
ATP synthase subunit f, mitochondrial: Xp
ATP synthase subunit g, mitochondrial: Yq
ATP synthase-coupling factor 6, mitochondrial: Zr
ATP synthase subunit ATP5MPL, mitochondrial: 0s
ATP synthase membrane subunit DAPIT, mitochondrial: 1t
ATP synthase protein 8: uv

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

2
AA

3
AB

4
AC

D
D

E
E

F
F

5
AD

6
AE

7
AF

G
G

8
AG

H
H

9
AH

I
I

a
AI

J
J

b
AJ

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

c
AK

d
AL

e
AM

f
AN

g
AO

h
AP

i
AQ

j
AR

S
S

k
AS

T
a

l
Aa

U
b

m
Ab

V
d

n
Ad

W
e

o
Ae

X
f

p
Af

Y
g

q
Ag

Z
h

r
Ah

0
j

s
Aj

1
k

t
Ak

u
A8

v
8

ATP synthase subunit alpha, mitochondrial

ATP synthase subunit beta, mitochondrial

ATP synthase subunit gamma, mitochondrial

ATP synthase subunit delta, mitochondrial

ATP synthase subunit epsilon, mitochondrial

ATPase inhibitor, mitochondrial

ATP synthase F(0) complex subunit C2, mitochondrial

ATP synthase subunit O, mitochondrial

ATP synthase subunit a

ATP synthase F(0) complex subunit B1, mitochondrial

ATP synthase subunit d, mitochondrial

ATP synthase subunit e, mitochondrial

ATP synthase subunit f, mitochondrial

ATP synthase subunit g, mitochondrial

ATP synthase-coupling factor 6, mitochondrial

ATP synthase subunit ATP5MPL, mitochondrial

ATP synthase membrane subunit DAPIT, mitochondrial

ATP synthase protein 8

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