SMTL ID : 5lqx.1

Structure of F-ATPase from Pichia angusta, state3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 7 residues within 4Å: Chain E: R.173, Q.174, T.178, A.179, R.364, P.365 Ligands: MG.2 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.174, E:K.177, E:T.178

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain E: T.178 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain F: T.178 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain G: T.178 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain H: T.162 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain J: T.162 Ligands: ADP.10 No protein-ligand interaction detected (PLIP)

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

ADP.3: 13 residues within 4Å: Chain F: D.172, R.173, Q.174, T.175, G.176, K.177, T.178, A.179, R.364, Q.432, K.433, Q.434 Ligands: MG.4 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:D.172, F:Q.174, F:T.175, F:G.176, F:K.177, F:T.178, F:Q.432, F:Q.434 ADP.5: 14 residues within 4Å: Chain G: D.172, R.173, Q.174, T.175, G.176, K.177, T.178, A.179, R.364, Q.432, K.433, Q.434 Chain J: R.354 Ligands: MG.6 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:D.172, G:Q.174, G:T.175, G:G.176, G:K.177, G:T.178, G:Q.432, G:Q.434 ADP.7: 13 residues within 4Å: Chain G: S.374, R.375 Chain H: G.156, A.157, G.158, V.159, G.160, K.161, T.162, V.163, Y.343, A.419 Ligands: MG.8 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:G.156, H:G.158, H:V.159, H:G.160, H:K.161, H:T.162 ADP.9: 10 residues within 4Å: Chain I: G.156, A.157, G.158, V.159, G.160, K.161, T.162, V.163, Y.343, A.419 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:G.156, I:G.158, I:V.159, I:G.160, I:K.161, I:T.162 ADP.10: 11 residues within 4Å: Chain J: G.156, A.157, G.158, V.159, G.160, K.161, T.162, V.163, Y.343, A.419 Ligands: MG.11 6 PLIP interactions: 6 interactions with chain J Hydrogen bonds: J:G.156, J:G.158, J:V.159, J:G.160, J:K.161, J:T.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vinothkumar, K.R. et al., Structure of the mitochondrial ATP synthase fromPichia angustadetermined by electron cryo-microscopy. Proc. Natl. Acad. Sci. U.S.A. (2016)

Release Date

2016-11-16

Peptides

ATP synthase subunit f: A
ATP synthase AAP1 subunit: B
ATP synthase subunit a: C
ATP synthase subunit b: D
ATP synthase alpha subunit: EFG
ATP synthase beta subunit: HIJ
ATP synthase gamma subunit: K
ATP synthase delta subunit: L
ATP synthase epsilon subunit: M
ATP synthase inhibitor protein IF1: N
ATP synthase subunit c: OPQRSTUVWX
ATP synthase OSCP subunit: Y
ATP synthase subunit b: Z
ATP synthase subunit d: 0
ATP synthase subunit h: 1
ATP synthase subunit a: 2
ATP synthase subunit a: 3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

E
A

F
B

G
C

H
D

I
E

J
F

K
G

L
H

M
I

N
J

O
K

P
L

Q
M

R
N

S
O

T
P

U
Q

V
R

W
S

X
T

Y
U

Z
V

0
W

1
X

2
Y

3
Z

Membrane

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

ATP synthase AAP1 subunit

ATP synthase subunit a

ATP synthase subunit b

ATP synthase alpha subunit

ATP synthase beta subunit

ATP synthase gamma subunit

ATP synthase delta subunit

ATP synthase epsilon subunit

ATP synthase inhibitor protein IF1

ATP synthase subunit c

ATP synthase OSCP subunit

ATP synthase subunit b

ATP synthase subunit d

ATP synthase subunit h

ATP synthase subunit a

ATP synthase subunit a

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