SMTL ID : 6f5d.1

Trypanosoma brucei F1-ATPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

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

Ligands

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

ADP.1: 13 residues within 4Å: Chain A: D.183, Q.185, T.186, G.187, K.188, T.189, S.190, F.370, R.375, P.376, Q.440, K.441 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Q.185, A:Q.185, A:T.186, A:G.187, A:K.188, A:T.189, A:S.190, A:S.190, A:R.375, A:Q.440 Water bridges: A:K.188, A:T.189, A:T.189 Salt bridges: A:K.188 pi-Cation interactions: A:K.441 ADP.3: 16 residues within 4Å: Chain B: D.183, R.184, Q.185, T.186, G.187, K.188, T.189, S.190, F.370, R.375, P.376, Q.440, K.441 Chain E: R.361, D.364 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.185, B:T.186, B:G.187, B:K.188, B:T.189, B:T.189, B:S.190, B:S.190, B:Q.440 Water bridges: B:K.188, B:K.188, B:K.188, B:T.189, B:D.282 Salt bridges: B:K.188 ADP.5: 16 residues within 4Å: Chain C: D.183, R.184, Q.185, T.186, G.187, K.188, T.189, S.190, F.370, R.375, P.376, Q.440, K.441 Chain F: R.361, D.364 Ligands: MG.6 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:Q.185, C:Q.185, C:T.186, C:G.187, C:K.188, C:T.189, C:T.189, C:S.190, C:S.190, C:R.375, C:Q.440, F:D.364 Water bridges: C:K.188, C:K.188, C:K.188, C:T.189, C:T.189 Salt bridges: C:K.188 ADP.7: 17 residues within 4Å: Chain C: V.384, S.385, R.386 Chain D: G.163, A.164, G.165, V.166, G.167, K.168, T.169, V.170, Y.350, F.423, A.426, F.429, T.430 Ligands: MG.8 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.163, D:G.165, D:V.166, D:G.167, D:K.168, D:T.169, D:T.169, D:V.170 Water bridges: D:R.195, D:E.198, C:R.386, C:R.386 Salt bridges: D:K.168, C:R.386, C:R.386 pi-Stacking: D:Y.350, D:Y.350 ADP.9: 10 residues within 4Å: Chain E: G.165, G.167, K.168, T.169, V.170, Y.350, F.423, A.426, F.429, T.430 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.165, E:V.166, E:G.167, E:K.168, E:T.169, E:T.169, E:V.170 Salt bridges: E:K.168 pi-Stacking: E:Y.350, E:Y.350 ADP.10: 15 residues within 4Å: Chain B: V.384, R.386 Chain F: A.164, G.165, V.166, G.167, K.168, T.169, V.170, Y.350, F.423, A.426, F.429, T.430 Ligands: MG.11 16 PLIP interactions: 1 interactions with chain B, 15 interactions with chain F Hydrogen bonds: B:R.386, F:G.163, F:G.165, F:V.166, F:G.167, F:K.168, F:T.169, F:T.169, F:V.170 Water bridges: F:R.195, F:R.195, F:R.195, F:R.195 Salt bridges: F:K.168 pi-Stacking: F:Y.350, F:Y.350

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.189, D.282 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.189, H2O.1, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain B: T.189, D.282 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.189, H2O.1, H2O.1, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain C: T.189, D.282 Ligands: ADP.5 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.189, H2O.1, H2O.1, H2O.1, H2O.1 MG.8: 3 residues within 4Å: Chain D: T.169, R.195 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.169, H2O.1, H2O.1, H2O.1, H2O.1 MG.11: 4 residues within 4Å: Chain F: T.169, E.194, R.195 Ligands: ADP.10 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.169, H2O.1, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Montgomery, M.G. et al., ATP synthase fromTrypanosoma bruceihas an elaborated canonical F1-domain and conventional catalytic sites. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-02-21

Peptides

ATP synthase subunit alpha, mitochondrial: ABC
ATP synthase subunit beta, mitochondrial: DEF
ATP synthase gamma subunit: G
ATP synthase subunit delta, mitochondrial: H
ATP synthase subunit epsilon, mitochondrial: I
ATP synthase subunit p18, mitochondrial: JKL

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

ATP synthase subunit alpha, mitochondrial

ATP synthase subunit beta, mitochondrial

ATP synthase gamma subunit

ATP synthase subunit delta, mitochondrial

ATP synthase subunit epsilon, mitochondrial

ATP synthase subunit p18, mitochondrial