SMTL ID : 2hld.1 (2 other biounits)

Crystal structure of yeast mitochondrial F1-ATPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

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

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

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

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

ANP.2: 14 residues within 4Å: Chain A: R.173, Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, P.365, Q.432, Q.434 Chain D: Y.368 Ligands: MG.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.174, A:T.175, A:G.176, A:K.177, A:K.177, A:T.178, A:T.178, A:A.179, A:Q.432, A:Q.434, A:Q.434 Water bridges: A:Q.174, A:Q.174 ANP.4: 14 residues within 4Å: Chain B: D.172, R.173, Q.174, T.175, G.176, K.177, T.178, A.179, F.359, R.364, P.365, Q.432, Q.434 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:Q.174, B:Q.174, B:T.175, B:T.175, B:G.176, B:K.177, B:K.177, B:T.178, B:A.179, B:R.364, B:Q.432, B:Q.434, B:Q.434 ANP.6: 15 residues within 4Å: Chain C: R.173, 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 F: Y.368 Ligands: MG.5 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Q.174, C:T.175, C:T.175, C:G.176, C:K.177, C:K.177, C:T.178, C:A.179, C:Q.432, C:Q.434 ANP.8: 18 residues within 4Å: Chain C: 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.311, Y.345, F.418, A.421, F.424, T.425 Ligands: MG.7 13 PLIP interactions: 10 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: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.10: 20 residues within 4Å: Chain B: I.345, S.346, V.373, 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, F.418, A.421, F.424, T.425 Ligands: MG.9 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain F Hydrogen bonds: B:S.346, B:R.375, B:R.375, F:G.160, F:V.161, F:G.162, F:K.163, F:K.163, F:K.163, F:T.164, F:V.165, F:R.190, F:R.190 Salt bridges: B:R.375 pi-Stacking: F:Y.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kabaleeswaran, V. et al., Novel features of the rotary catalytic mechanism revealed in the structure of yeast F(1) ATPase. Embo J. (2006)

Release Date

2006-11-28

Peptides

ATP synthase alpha chain, mitochondrial: ABC
ATP synthase beta chain, mitochondrial: DEF
ATP synthase gamma chain, mitochondrial: G
ATP synthase delta chain, mitochondrial: H
ATP synthase epsilon chain, mitochondrial: 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 alpha chain, mitochondrial

ATP synthase beta chain, mitochondrial

ATP synthase gamma chain, mitochondrial

ATP synthase delta chain, mitochondrial

ATP synthase epsilon chain, mitochondrial

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