SMTL ID : 3zry.1 (1 other biounit)

Rotor architecture in the F(1)-c(10)-ring complex of the yeast F-ATP synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 6.50 Å

Oligo State

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

Ligands

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

ANP.1: 14 residues within 4Å: Chain A: R.173, Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, Q.432, N.433, Q.434 Chain D: Y.368 Ligands: MG.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.174, A:T.175, A:G.176, A:K.177, A:K.177, A:K.177, A:T.178, A:A.179, A:Q.432, A:Q.434, D:Y.368 ANP.3: 15 residues within 4Å: Chain B: 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 Chain E: R.356 Ligands: MG.4 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:Q.174, B:Q.174, B:T.175, B:T.175, B:G.176, B:K.177, B:K.177, B:K.177, B:T.178, B:T.178, B:A.179, B:E.330, B:R.364, B:Q.432, E:R.356 pi-Stacking: B:F.359 pi-Cation interactions: B:R.364 ANP.5: 14 residues within 4Å: Chain C: R.173, Q.174, T.175, G.176, K.177, T.178, A.179, E.330, R.364, P.365, Q.432, N.433, Q.434 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Q.174, C:Q.174, C:T.175, C:G.176, C:K.177, C:K.177, C:K.177, C:T.178, C:A.179, C:E.330, C:E.330, C:Q.432, C:Q.434 ANP.7: 17 residues within 4Å: Chain C: S.346, R.375 Chain D: 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: 12 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.160, D:V.161, D:G.162, D:K.163, D:K.163, D:K.163, D:T.164, D:T.164, D:V.165, D:R.190, D:R.190, C:R.375, C:R.375 pi-Stacking: D:Y.345 Salt bridges: C:R.375 ANP.9: 17 residues within 4Å: Chain B: R.375 Chain F: G.158, A.159, G.160, V.161, G.162, K.163, T.164, V.165, E.189, R.190, Y.345, P.346, F.418, A.421, F.424 Ligands: MG.10 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:G.160, F:V.161, F:G.162, F:K.163, F:K.163, F:K.163, F:T.164, F:T.164, F:T.164, F:V.165, F:R.190, F:R.190, B:R.375, B:R.375 Salt bridges: B:R.375

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.178 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.178 MG.4: 3 residues within 4Å: Chain B: T.178, D.271 Ligands: ANP.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: ANP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.178 MG.8: 6 residues within 4Å: Chain C: R.375 Chain D: T.164, E.189, R.190, E.193 Ligands: ANP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.164, D:E.193 MG.10: 6 residues within 4Å: Chain F: K.163, T.164, E.189, D.256, N.257 Ligands: ANP.9 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.164, F:E.189, F:D.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Giraud, M.-F. et al., Rotor Architecture in the Yeast and Bovine F(1)-C-Ring Complexes of F-ATP Synthase. J.Struct.Biol. (2012)

Release Date

2012-01-18

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 CATALYTIC SECTOR F1 EPSILON SUBUNIT: I

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

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

Related Entries With Identical Sequence