SMTL ID : 6b8h.1

Mosaic model of yeast mitochondrial ATP synthase monomer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-20-2-2-2-2-2-2-2-2-2-6-6-2-2-2-2-2-mer

Ligands

10 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 14 residues within 4Å: Chain T: R.173, Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, P.365, Q.432, Q.434 Chain W: Y.368 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain T Hydrogen bonds: T:Q.174, T:T.175, T:G.176, T:K.177, T:K.177, T:T.178, T:T.178, T:A.179, T:Q.432, T:Q.434 ANP.3: 14 residues within 4Å: Chain U: D.172, R.173, Q.174, T.175, G.176, K.177, T.178, A.179, E.330, F.359, R.364, Q.432, Q.434 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain U Hydrogen bonds: U:Q.174, U:Q.174, U:T.175, U:T.175, U:G.176, U:K.177, U:K.177, U:T.178, U:A.179, U:E.330, U:R.364, U:Q.432, U:Q.434 pi-Stacking: U:F.359 pi-Cation interactions: U:R.364 ANP.5: 15 residues within 4Å: Chain V: R.173, Q.174, T.175, G.176, K.177, T.178, A.179, E.330, F.359, R.364, Q.432, N.433, Q.434 Chain Y: Y.368 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain V Hydrogen bonds: V:Q.174, V:T.175, V:G.176, V:K.177, V:K.177, V:T.178, V:A.179, V:E.330, V:Q.432, V:Q.434 ANP.7: 17 residues within 4Å: Chain V: S.346, R.375 Chain W: G.158, A.159, G.160, V.161, G.162, K.163, T.164, V.165, E.189, R.190, Y.345, F.418, A.421, F.424 Ligands: MG.8 15 PLIP interactions: 11 interactions with chain W, 4 interactions with chain V Hydrogen bonds: W:G.160, W:V.161, W:G.162, W:K.163, W:K.163, W:T.164, W:V.165, W:R.190, W:R.190, V:S.346, V:R.375, V:R.375 pi-Stacking: W:Y.345, W:Y.345 Salt bridges: V:R.375 ANP.9: 19 residues within 4Å: Chain U: I.345, S.346, V.373, R.375 Chain Y: G.158, A.159, G.160, V.161, G.162, K.163, T.164, V.165, E.189, R.190, Y.345, F.418, A.421, F.424 Ligands: MG.10 13 PLIP interactions: 10 interactions with chain Y, 3 interactions with chain U Hydrogen bonds: Y:G.160, Y:V.161, Y:G.162, Y:K.163, Y:K.163, Y:K.163, Y:T.164, Y:V.165, Y:R.190, Y:R.190, U:R.375, U:R.375 Salt bridges: U:R.375 ANP.11: 14 residues within 4Å: Ligands: MG.12 Chain n: R.173, Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, P.365, Q.432, Q.434 Chain q: Y.368 10 PLIP interactions: 10 interactions with chain n Hydrogen bonds: n:Q.174, n:T.175, n:G.176, n:K.177, n:K.177, n:T.178, n:T.178, n:A.179, n:Q.432, n:Q.434 ANP.13: 14 residues within 4Å: Ligands: MG.14 Chain o: D.172, R.173, Q.174, T.175, G.176, K.177, T.178, A.179, E.330, F.359, R.364, Q.432, Q.434 15 PLIP interactions: 15 interactions with chain o Hydrogen bonds: o:Q.174, o:Q.174, o:T.175, o:T.175, o:G.176, o:K.177, o:K.177, o:T.178, o:A.179, o:E.330, o:R.364, o:Q.432, o:Q.434 pi-Stacking: o:F.359 pi-Cation interactions: o:R.364 ANP.15: 15 residues within 4Å: Ligands: MG.16 Chain p: R.173, Q.174, T.175, G.176, K.177, T.178, A.179, E.330, F.359, R.364, Q.432, N.433, Q.434 Chain s: Y.368 11 PLIP interactions: 11 interactions with chain p Hydrogen bonds: p:Q.174, p:T.175, p:G.176, p:K.177, p:K.177, p:T.178, p:T.178, p:A.179, p:E.330, p:Q.432, p:Q.434 ANP.17: 17 residues within 4Å: Ligands: MG.18 Chain p: S.346, R.375 Chain q: G.158, A.159, G.160, V.161, G.162, K.163, T.164, V.165, E.189, R.190, Y.345, F.418, A.421, F.424 15 PLIP interactions: 11 interactions with chain q, 4 interactions with chain p Hydrogen bonds: q:G.160, q:V.161, q:G.162, q:K.163, q:K.163, q:T.164, q:V.165, q:R.190, q:R.190, p:S.346, p:R.375, p:R.375 pi-Stacking: q:Y.345, q:Y.345 Salt bridges: p:R.375 ANP.19: 19 residues within 4Å: Ligands: MG.20 Chain o: I.345, S.346, V.373, R.375 Chain s: G.158, A.159, G.160, V.161, G.162, K.163, T.164, V.165, E.189, R.190, Y.345, F.418, A.421, F.424 13 PLIP interactions: 10 interactions with chain s, 3 interactions with chain o Hydrogen bonds: s:G.160, s:V.161, s:G.162, s:K.163, s:K.163, s:K.163, s:T.164, s:V.165, s:R.190, s:R.190, o:R.375, o:R.375 Salt bridges: o:R.375

10 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain T: T.178 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:T.178 MG.4: 2 residues within 4Å: Chain U: T.178 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:T.178 MG.6: 2 residues within 4Å: Chain V: T.178 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:T.178 MG.8: 5 residues within 4Å: Chain W: T.164, E.189, R.190, E.193 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain W Metal complexes: W:T.164 MG.10: 5 residues within 4Å: Chain Y: T.164, E.189, R.190, E.193 Ligands: ANP.9 2 PLIP interactions: 2 interactions with chain Y Metal complexes: Y:T.164, Y:E.189 MG.12: 2 residues within 4Å: Ligands: ANP.11 Chain n: T.178 1 PLIP interactions: 1 interactions with chain n Metal complexes: n:T.178 MG.14: 2 residues within 4Å: Ligands: ANP.13 Chain o: T.178 1 PLIP interactions: 1 interactions with chain o Metal complexes: o:T.178 MG.16: 2 residues within 4Å: Ligands: ANP.15 Chain p: T.178 1 PLIP interactions: 1 interactions with chain p Metal complexes: p:T.178 MG.18: 5 residues within 4Å: Ligands: ANP.17 Chain q: T.164, E.189, R.190, E.193 1 PLIP interactions: 1 interactions with chain q Metal complexes: q:T.164 MG.20: 5 residues within 4Å: Ligands: ANP.19 Chain s: T.164, E.189, R.190, E.193 2 PLIP interactions: 2 interactions with chain s Metal complexes: s:T.164, s:E.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, H. et al., Atomic model for the dimeric FO region of mitochondrial ATP synthase. Science (2017)

Release Date

2018-01-17

Peptides

ATP synthase subunit 9, mitochondrial: ABCDEFGHIJ456789abcd
ATP synthase protein 8: Ke
ATP synthase subunit a: Lf
ATP synthase subunit 4, mitochondrial: Mg
ATP synthase subunit d, mitochondrial: Nh
ATP synthase subunit e, mitochondrial: Oi
ATP synthase subunit f, mitochondrial: Pj
AATP synthase subunit g: Qk
ATP synthase subunit J, mitochondrial: Rl
ATP synthase subunit K, mitochondrial: Sm
ATP synthase subunit alpha, mitochondrial: TUVnop
ATP synthase subunit beta, mitochondrial: WXYqrs
ATP synthase subunit gamma, mitochondrial: Zt
ATP synthase subunit delta, mitochondrial: 0u
ATP synthase catalytic sector F1 epsilon subunit: 1v
ATP synthase subunit 5, mitochondrial: 2w
ATP synthase subunit h: 3x

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
5

F
6

G
7

H
8

I
9

J
0

4
L

5
M

6
N

7
P

8
Q

9
R

a
S

b
T

c
U

d
J

K
A

e
V

L
a

f
p

M
b

g
q

N
d

h
r

O
e

i
s

P
f

j
t

Q
g

k
u

R
i

l
w

S
k

m
x

T
K

U
B

V
C

n
n

o
W

p
X

W
D

X
E

Y
F

q
Y

r
Z

s
c

Z
G

t
j

0
H

u
l

1
I

v
m

2
O

w
o

3
h

x
v

ATP synthase subunit 9, mitochondrial

ATP synthase protein 8

ATP synthase subunit a

ATP synthase subunit 4, mitochondrial

ATP synthase subunit d, mitochondrial

ATP synthase subunit e, mitochondrial

ATP synthase subunit f, mitochondrial

AATP synthase subunit g

ATP synthase subunit J, mitochondrial

ATP synthase subunit K, mitochondrial

ATP synthase subunit alpha, mitochondrial

ATP synthase subunit beta, mitochondrial

ATP synthase subunit gamma, mitochondrial

ATP synthase subunit delta, mitochondrial

ATP synthase catalytic sector F1 epsilon subunit

ATP synthase subunit 5, mitochondrial

ATP synthase subunit h

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