SMTL ID : 2wpd.1

The Mg.ADP inhibited state of the yeast F1c10 ATP synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.43 Å

Oligo State

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

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: Q.174, T.175, G.176, K.177, T.178, A.179, E.330, F.359, R.364, P.365, Q.432, Q.434 Chain D: S.355 Ligands: MG.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.174, A:T.175, A:G.176, A:K.177, A:T.178, A:A.179, A:Q.432, A:Q.434, D:S.355 Salt bridges: A:K.177, A:K.177 pi-Stacking: A:F.359 ATP.3: 13 residues within 4Å: Chain B: Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, P.365, Q.432, N.433, Q.434 Ligands: MG.4 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.175, B:G.176, B:K.177, B:T.178, B:A.179, B:R.364, B:Q.432, B:Q.434 Salt bridges: B:K.177, B:K.177 ATP.5: 13 residues within 4Å: Chain C: Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, Q.432, Q.434 Chain F: S.355, Y.368 Ligands: MG.6 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.174, C:Q.174, C:T.175, C:T.175, C:G.176, C:K.177, C:T.178, C:A.179, C:Q.432, F:S.355 Salt bridges: C:K.177, C:K.177

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.178, Q.210, D.271 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.178 MG.4: 4 residues within 4Å: Chain B: K.177, T.178, D.271 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.178 MG.6: 3 residues within 4Å: Chain C: T.178, D.271 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.178 MG.8: 5 residues within 4Å: Chain D: T.164, E.189, R.190, E.193 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.164 MG.10: 4 residues within 4Å: Chain F: T.164, E.189, D.256 Ligands: ADP.9 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.164, F:E.189

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

ADP.7: 14 residues within 4Å: Chain C: S.374, R.375 Chain D: G.158, A.159, G.160, V.161, G.162, K.163, T.164, V.165, Y.345, F.418, T.425 Ligands: MG.8 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:R.375, D:G.158, D:G.160, D:V.161, D:G.162, D:K.163, D:T.164, D:T.164, D:V.165 Salt bridges: C:R.375, C:R.375, D:K.163 ADP.9: 14 residues within 4Å: Chain B: V.373, S.374, R.375 Chain F: G.160, V.161, G.162, K.163, T.164, V.165, Y.345, F.418, F.424, T.425 Ligands: MG.10 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain F Hydrogen bonds: B:S.374, F:G.160, F:V.161, F:G.162, F:K.163, F:T.164, F:V.165 Salt bridges: B:R.375, B:R.375, F:K.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dautant, A. et al., Crystal Structure of the Mg.Adp-Inhibited State of the Yeast F1C10-ATP Synthase. J.Biol.Chem. (2010)

Release Date

2010-07-07

Peptides

ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL: ABC
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL: DEF
ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL: G
ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL: H
ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL: I
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL: JKLMNOPQRS

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
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

Membrane

We predict this structure to be a membrane protein.
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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

ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL

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