SMTL ID : 5fl7.1

Structure of the F1c10 complex from Yarrowia lipolytica ATP synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 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.198, T.199, G.200, K.201, T.202, Q.203, F.383, R.388, P.389, Q.456, K.457, Q.458 Chain D: S.386 Ligands: MG.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.198, A:T.199, A:G.200, A:K.201, A:T.202, A:T.202, A:Q.203, A:Q.456, A:Q.458, D:S.386 Water bridges: A:K.201, A:K.201, A:T.202 Salt bridges: A:K.201, A:K.201 pi-Stacking: A:F.383 ATP.3: 16 residues within 4Å: Chain B: R.197, Q.198, T.199, G.200, K.201, T.202, Q.203, F.383, R.388, P.389, Q.456, K.457, Q.458 Chain E: R.387, D.390 Ligands: MG.4 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:Q.198, B:T.199, B:G.200, B:K.201, B:T.202, B:T.202, B:Q.203, B:E.354, B:Q.456, E:R.387, E:D.390 Water bridges: B:K.201, B:K.201, B:T.202 Salt bridges: B:K.201, B:K.201 ATP.5: 15 residues within 4Å: Chain C: R.197, Q.198, T.199, G.200, K.201, T.202, Q.203, F.383, R.388, P.389, Q.456, K.457, Q.458 Chain F: D.390 Ligands: MG.6 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.198, C:T.199, C:G.200, C:K.201, C:T.202, C:Q.203, C:Q.456, F:D.390 Water bridges: C:K.201, C:K.201, C:T.202 Salt bridges: C:K.201, C:K.201 pi-Stacking: C:F.383

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.202, D.295 Ligands: ATP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.202, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain B: T.202, D.295 Ligands: ATP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.202, H2O.1, H2O.1, H2O.1 MG.6: 2 residues within 4Å: Chain C: T.202 Ligands: ATP.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.202, H2O.1, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain D: T.195, R.221, E.224 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.195, H2O.1, H2O.1, H2O.1, H2O.1 MG.10: 3 residues within 4Å: Chain F: T.195, E.220 Ligands: ADP.9 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.195, H2O.1, H2O.1, H2O.1, H2O.1

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

ADP.7: 16 residues within 4Å: Chain C: V.397, S.398, R.399 Chain D: G.189, A.190, G.191, V.192, G.193, K.194, T.195, V.196, Y.376, F.449, A.452, F.455 Ligands: MG.8 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.191, D:V.192, D:G.193, D:K.194, D:T.195, D:V.196, C:S.398 Water bridges: D:T.195, D:T.195, D:T.195, D:T.195, D:T.195 Salt bridges: D:K.194, C:R.399, C:R.399 pi-Stacking: D:Y.376, D:F.455 ADP.9: 14 residues within 4Å: Chain B: V.397, R.399 Chain F: A.190, G.191, V.192, G.193, K.194, T.195, V.196, R.221, Y.376, F.449, F.455 Ligands: MG.10 15 PLIP interactions: 13 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.191, F:G.193, F:K.194, F:T.195, F:T.195, F:V.196, F:R.221 Water bridges: F:K.194, F:K.194, F:K.194, F:T.195 Salt bridges: F:K.194, B:R.399, B:R.399 pi-Stacking: F:Y.376

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hahn, A. et al., Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology. Mol.Cell (2016)

Release Date

2016-06-29

Peptides

ATP SYNTHASE SUBUNIT ALPHA: ABC
ATP SYNTHASE SUBUNIT BETA: DEF
ATP SYNTHASE SUBUNIT GAMMA CHAIN, MITOCHONDRIAL: G
ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL: H
ATP SYNTHASE EPSILON CHAIN, 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
K

K
L

L
M

M
N

N
O

O
P

P
Q

Q
R

R
S

S
T

Membrane

We predict this structure to be a membrane protein.
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ATP SYNTHASE SUBUNIT ALPHA

ATP SYNTHASE SUBUNIT BETA

ATP SYNTHASE SUBUNIT GAMMA CHAIN, MITOCHONDRIAL

ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL

ATP SYNTHASE EPSILON CHAIN, MITOCHONDRIAL

ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL

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