SMTL ID : 2xnd.1

Crystal structure of bovine F1-c8 sub-complex of ATP Synthase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

hetero-3-3-1-1-1-8-mer

Ligands

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

ANP.1: 15 residues within 4Å: Chain A: D.152, R.153, Q.154, T.155, G.156, K.157, T.158, S.159, F.339, R.344, P.345, Q.412, Q.414 Chain D: S.347 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.154, A:T.155, A:G.156, A:K.157, A:K.157, A:T.158, A:S.159, A:S.159, A:Q.412 pi-Stacking: A:F.339 ANP.3: 15 residues within 4Å: Chain B: D.152, R.153, Q.154, T.155, G.156, K.157, T.158, S.159, F.339, R.344, Q.412, Q.414 Chain E: R.348, D.351 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Q.154, B:Q.154, B:Q.154, B:T.155, B:G.156, B:K.157, B:K.157, B:T.158, B:S.159, B:S.159, B:R.344, B:Q.412 ANP.6: 15 residues within 4Å: Chain C: D.152, R.153, Q.154, T.155, G.156, K.157, T.158, S.159, E.310, F.339, R.344, Q.412, Q.414 Chain F: Y.360 Ligands: MG.7 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.154, C:Q.154, C:T.155, C:G.156, C:K.157, C:K.157, C:T.158, C:S.159, C:S.159, C:E.310, C:E.310, C:Q.412, C:Q.414, C:Q.414, F:Y.360 ANP.8: 20 residues within 4Å: Chain C: S.326, S.354, R.355 Chain D: G.149, A.150, G.151, V.152, G.153, K.154, T.155, V.156, E.180, R.181, Y.303, Y.337, F.410, A.413, F.416, T.417 Ligands: MG.9 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.149, D:G.151, D:V.152, D:G.153, D:K.154, D:K.154, D:T.155, D:T.155, D:V.156, D:R.181, D:R.181, D:Y.337, C:S.354, C:R.355, C:R.355 pi-Stacking: D:Y.337, D:Y.337, D:F.416 Salt bridges: C:R.355 ANP.11: 20 residues within 4Å: Chain B: I.325, S.326, R.355 Chain F: G.149, A.150, G.151, V.152, G.153, K.154, T.155, V.156, E.180, R.181, Y.303, Y.337, F.410, A.413, F.416, T.417 Ligands: MG.12 17 PLIP interactions: 13 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:G.151, F:V.152, F:G.153, F:K.154, F:K.154, F:T.155, F:T.155, F:V.156, F:R.181, F:R.181, F:Y.337, B:R.355, B:R.355, B:R.355 pi-Stacking: F:Y.337, F:Y.337 Salt bridges: B:R.355

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.158, D.251 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.158 MG.4: 2 residues within 4Å: Chain B: T.158 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.158 MG.7: 3 residues within 4Å: Chain C: T.158, D.251 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.158 MG.9: 4 residues within 4Å: Chain D: T.155, E.180, D.248 Ligands: ANP.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.155, D:E.180 MG.12: 5 residues within 4Å: Chain F: T.155, E.180, R.181, E.184 Ligands: ANP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.155

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain B: M.44, V.111, G.112, Y.226, Y.230, R.286 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.111, B:Y.226, B:Y.226, B:R.286

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 5 residues within 4Å: Chain A: R.355 Chain E: K.154, R.181, D.248, R.252 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Salt bridges: E:K.154, E:R.181, E:R.252, A:R.355

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watt, I.N. et al., Bioenergetic Cost of Making an Adenosine Triphosphate Molecule in Animal Mitochondria. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-09-15

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 LIPID-BINDING PROTEIN, MITOCHONDRIAL: JKLMNOPQ

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

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 LIPID-BINDING PROTEIN, MITOCHONDRIAL

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