- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-2-2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-3-3-1-1-1-3-1-10-mer
- Ligands
- 14 x CDL: CARDIOLIPIN(Non-covalent)
- 3 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
3PE.3: 25 residues within 4Å:- Chain A: V.26, Y.30, K.33
- Chain B: L.117, G.118, Q.120
- Chain C: F.173, Y.174, V.176, F.177, C.178
- Chain N: L.117, Y.144
- Chain S: P.35, M.38, I.39, N.42, A.43, R.44, L.46
- Ligands: CDL.1, CDL.2, CDL.20, CDL.21, 3PE.22
9 PLIP interactions:3 interactions with chain S, 1 interactions with chain B, 2 interactions with chain A, 3 interactions with chain C- Hydrophobic interactions: S:M.38, S:I.39, A:Y.30, C:Y.174, C:F.177, C:F.177
- Hydrogen bonds: S:A.43, B:Q.120
- Salt bridges: A:K.33
3PE.14: 9 residues within 4Å:- Chain F: Q.2, W.5
- Chain G: V.2, L.3, F.4, S.5, S.10, L.12
- Chain J: R.10
3 PLIP interactions:2 interactions with chain G, 1 interactions with chain J- Hydrogen bonds: G:V.2, G:S.5
- Salt bridges: J:R.10
3PE.22: 12 residues within 4Å:- Chain B: L.117, Y.144
- Chain M: V.26, Y.30, K.33
- Chain N: L.117, G.118, Q.120
- Ligands: CDL.1, 3PE.3, CDL.20, CDL.21
5 PLIP interactions:1 interactions with chain N, 3 interactions with chain M, 1 interactions with chain B- Hydrogen bonds: N:Q.120
- Hydrophobic interactions: M:V.26, M:Y.30, B:L.117
- Salt bridges: M:K.33
- 4 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
PC1.5: 39 residues within 4Å:- Chain C: L.15, L.16, Y.19, L.68, Y.69, L.71, I.72, L.73, Y.74, Y.166, Y.195, Y.199, L.203
- Chain G: F.33, W.43, A.44, L.45, P.46, L.51, Y.52, M.55, I.56, P.57, I.59, Y.60, F.61, R.64
- Chain Q: L.29, V.30, F.31
- Chain S: M.1, L.2, F.23, S.26, V.27, F.29, W.30, Y.34, M.37
16 PLIP interactions:5 interactions with chain C, 6 interactions with chain S, 5 interactions with chain G- Hydrophobic interactions: C:Y.69, S:F.23, S:W.30, S:W.30, G:P.46, G:Y.52, G:P.57, G:Y.60, G:F.61
- Hydrogen bonds: C:L.73, C:Y.166, C:Y.199, S:W.30, S:Y.34, S:Y.34
- pi-Cation interactions: C:Y.166
PC1.15: 33 residues within 4Å:- Chain C: Y.83, F.86, C.87, F.90
- Chain D: T.34, L.37
- Chain J: F.32, T.33, I.35, F.36, L.37, K.39, H.40, M.41
- Chain L: T.85, W.86, A.89, V.90, Y.92, F.93, W.94
- Chain R: L.62, W.65, Y.66, R.69, S.70, L.73, F.74
- Ligands: CDL.4, CDL.8, CDL.10, CDL.19, CDL.25
14 PLIP interactions:4 interactions with chain C, 3 interactions with chain L, 6 interactions with chain J, 1 interactions with chain R- Hydrophobic interactions: C:Y.83, C:Y.83, C:F.86, C:F.86, L:W.86, J:F.32, J:F.32, J:F.36, R:Y.66
- Hydrogen bonds: L:W.94
- pi-Cation interactions: L:W.94
- Salt bridges: J:K.39, J:K.39, J:H.40
PC1.17: 17 residues within 4Å:- Chain C: C.104, F.106, F.107
- Chain K: C.49, V.52, L.53, R.63, Q.64, Y.65, V.75, A.79, M.83
- Chain L: R.25, Y.70
- Ligands: CDL.8, CDL.16, CDL.19
2 PLIP interactions:2 interactions with chain K- Hydrogen bonds: K:Q.64
- Salt bridges: K:R.63
PC1.24: 25 residues within 4Å:- Chain G: R.64, W.65, D.68, H.69, R.103, D.107
- Chain N: I.98, L.101, L.104, T.105, V.108
- Chain Q: M.78, L.83, W.86, C.90, I.93, Y.94, Q.95, Y.97, E.98
- Chain S: P.18, M.21, F.22, F.25, K.40
6 PLIP interactions:1 interactions with chain N, 2 interactions with chain G, 2 interactions with chain Q, 1 interactions with chain S- Hydrophobic interactions: N:L.104, Q:W.86, S:F.25
- Salt bridges: G:D.68, G:H.69, Q:E.98
- 2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)
LMT.11: 11 residues within 4Å:- Chain F: Y.30, W.33, L.34, Y.37, N.38, Q.41, K.42
- Chain K: W.91, Y.93, I.103
- Ligands: CDL.9
2 PLIP interactions:1 interactions with chain K, 1 interactions with chain F- Hydrophobic interactions: K:W.91
- Hydrogen bonds: F:N.38
LMT.18: 8 residues within 4Å:- Chain K: K.31, G.32, W.35, W.36, F.39, L.111, L.115, R.119
1 PLIP interactions:1 interactions with chain K- Hydrogen bonds: K:W.36
- 2 x Q7G: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside(Non-covalent)
Q7G.12: 10 residues within 4Å:- Chain F: G.110, Y.111, I.113, P.114, F.115
- Chain R: W.47, W.51, Y.52
- Ligands: CDL.7, CDL.10
4 PLIP interactions:4 interactions with chain R- Hydrophobic interactions: R:W.47, R:W.51, R:Y.52, R:Y.52
Q7G.23: 15 residues within 4Å:- Chain C: F.4, F.6
- Chain D: Y.46
- Chain O: Y.124, M.129, P.130, L.138, S.139, G.140, P.141, H.144
- Chain R: A.26, L.27
- Ligands: CDL.6, CDL.25
3 PLIP interactions:1 interactions with chain O, 1 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: O:G.140
- Hydrophobic interactions: C:F.4, D:Y.46
- 4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.26: 17 residues within 4Å:- Chain T: F.187, R.208, Q.209, T.210, G.211, K.212, T.213, S.214, E.365, F.394, R.399, P.400, Q.464, K.465
- Chain W: R.382, D.385
- Ligands: MG.27
13 PLIP interactions:13 interactions with chain T- Hydrogen bonds: T:Q.209, T:T.210, T:T.210, T:G.211, T:K.212, T:T.213, T:T.213, T:S.214, T:S.214, T:R.399
- Salt bridges: T:K.212, T:K.212
- pi-Cation interactions: T:K.465
ATP.28: 17 residues within 4Å:- Chain U: F.187, R.208, Q.209, T.210, G.211, K.212, T.213, S.214, F.394, R.399, P.400, Q.464, K.465
- Chain X: R.382, M.384, Y.394
- Ligands: MG.29
15 PLIP interactions:15 interactions with chain U- Hydrogen bonds: U:Q.209, U:Q.209, U:T.210, U:T.210, U:G.211, U:K.212, U:T.213, U:T.213, U:S.214, U:S.214, U:Q.464, U:K.465
- Salt bridges: U:K.212, U:K.212
- pi-Cation interactions: U:K.465
ATP.30: 17 residues within 4Å:- Chain V: F.187, D.207, R.208, Q.209, T.210, G.211, K.212, T.213, S.214, F.394, R.399, P.400, Q.464, K.465
- Chain Y: D.385, Y.394
- Ligands: MG.31
16 PLIP interactions:16 interactions with chain V- Hydrogen bonds: V:Q.209, V:Q.209, V:T.210, V:T.210, V:G.211, V:K.212, V:T.213, V:S.214, V:S.214, V:R.399, V:R.399, V:K.465
- Salt bridges: V:K.212, V:K.212
- pi-Cation interactions: V:K.465, V:K.465
ATP.32: 22 residues within 4Å:- Chain T: S.381, V.408, R.410
- Chain X: G.184, A.185, G.186, V.187, G.188, K.189, T.190, V.191, I.192, R.216, Y.337, Y.371, P.372, F.444, A.447, F.450, T.451, M.485
- Ligands: MG.33
14 PLIP interactions:11 interactions with chain X, 3 interactions with chain T- Hydrogen bonds: X:G.186, X:V.187, X:G.188, X:K.189, X:T.190, X:T.190, X:V.191
- Salt bridges: X:K.189, X:K.189, X:R.216, T:R.410, T:R.410, T:R.410
- pi-Stacking: X:Y.371
- 5 x MG: MAGNESIUM ION(Non-covalent)
MG.27: 4 residues within 4Å:- Chain T: T.213, N.249, D.306
- Ligands: ATP.26
2 PLIP interactions:2 interactions with chain T- Metal complexes: T:T.213, T:D.306
MG.29: 3 residues within 4Å:- Chain U: T.213, D.306
- Ligands: ATP.28
1 PLIP interactions:1 interactions with chain U- Metal complexes: U:T.213
MG.31: 3 residues within 4Å:- Chain V: T.213, D.306
- Ligands: ATP.30
No protein-ligand interaction detected (PLIP)MG.33: 4 residues within 4Å:- Chain X: T.190, R.216, E.219
- Ligands: ATP.32
1 PLIP interactions:1 interactions with chain X- Metal complexes: X:T.190
MG.35: 6 residues within 4Å:- Chain Y: T.190, E.215, R.216, E.219, D.282
- Ligands: ADP.34
1 PLIP interactions:1 interactions with chain Y- Metal complexes: Y:T.190
- 1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.34: 20 residues within 4Å:- Chain U: V.408, S.409, R.410
- Chain Y: G.184, A.185, G.186, V.187, G.188, K.189, T.190, V.191, R.216, Y.371, P.443, F.444, A.447, F.450, T.451, M.485
- Ligands: MG.35
12 PLIP interactions:9 interactions with chain Y, 3 interactions with chain U- Hydrogen bonds: Y:G.186, Y:G.188, Y:K.189, Y:T.190, Y:T.190, Y:V.191, Y:R.216, U:S.409
- Salt bridges: Y:K.189, U:R.410, U:R.410
- pi-Stacking: Y:Y.371
- 1 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)
UTP.36: 14 residues within 4Å:- Chain 0: N.76, Y.79, K.88
- Chain 6: R.82
- Chain 7: V.78, R.82
- Chain Z: N.208, E.209, E.210
- Chain a: R.82
- Chain b: R.82
- Chain c: R.82
- Chain d: R.82
- Chain e: R.82
14 PLIP interactions:5 interactions with chain 0, 1 interactions with chain 6, 2 interactions with chain d, 2 interactions with chain Z, 2 interactions with chain c, 1 interactions with chain 7, 1 interactions with chain e- Hydrogen bonds: 0:N.76, 0:Y.79, 6:R.82, d:R.82, Z:E.209, Z:E.210
- Salt bridges: 0:K.88, 0:K.88, 0:K.88, d:R.82, c:R.82, c:R.82, e:R.82
- pi-Cation interactions: 7:R.82
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gahura, O. et al., An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases. Nat Commun (2022)
- Release Date
- 2022-10-26
- Peptides
- subunit-e: AM
subunit-g: BN
ATP synthase subunit a: C
subunit-8: D
subunit-d: E
ATPTB1: F
subunit-f: G
ATPTB3: H
ATPTB4: I
subunit-i/j: J
ATPTB6: K
subunit-k: L
ATPTB11: O
ATPTB12: P
subunit-b: Q
ATPEG3: R
ATPEG4: S
ATP synthase subunit alpha, mitochondrial: TUV
ATP synthase subunit beta, mitochondrial: WXY
ATP synthase gamma subunit: Z
ATP synthase, epsilon chain, putative: 0
ATP synthase subunit epsilon, mitochondrial: 1
ATP synthase subunit p18, mitochondrial: 234
OSCP: 5
ATPase subunit 9, putative: 6789abcdef - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
LM
lB
MN
mC
aD
cE
dF
eG
fH
gI
hJ
iK
jL
kO
nP
oQ
pR
qS
rT
A1U
B1V
C1W
D1X
E1Y
F1Z
G10
H11
I12
J13
K14
L15
M16
O17
P18
Q19
R1a
S1b
T1c
U1d
V1e
W1f
X1 - Membrane
-
We predict this structure to be a membrane protein.
SMTL ID : 8apk.1
rotational state 3 of the Trypanosoma brucei mitochondrial ATP synthase dimer
subunit-e
Toggle Identical (AM)subunit-g
Toggle Identical (BN)ATP synthase subunit a
subunit-8
subunit-d
ATPTB1
subunit-f
ATPTB3
ATPTB4
subunit-i/j
ATPTB6
subunit-k
ATPTB11
ATPTB12
subunit-b
ATPEG3
ATPEG4
ATP synthase subunit alpha, mitochondrial
ATP synthase subunit beta, mitochondrial
ATP synthase gamma subunit
ATP synthase, epsilon chain, putative
ATP synthase subunit epsilon, mitochondrial
ATP synthase subunit p18, mitochondrial
Toggle Identical (23)OSCP
ATPase subunit 9, putative
Toggle Identical (6789abcdef)Related Entries With Identical Sequence
8ap6.1 | 8ap6.2 | 8ap6.3 | 8ap6.4 | 8ap6.5 | 8ap6.6 | 8ap6.7 | 8ap6.8 | 8ap6.9 | 8ap6.10 | 8ap6.11 | 8ap6.12 | 8ap6.13 | 8ap6.14 | 8ap6.15 | 8ap6.16 | 8ap6.17 | 8ap6.18 | 8ap6.19 | 8ap6.20 | 8ap6.21 | 8ap6.22 | 8ap6.23 | 8ap6.24 | 8ap6.25 | 8ap6.26 | 8ap6.27 | 8ap6.28 | 8ap6.29 | 8ap6.30 more...less...8ap6.31 | 8ap6.32 | 8ap6.33 | 8ap6.34 | 8ap6.35 | 8ap6.36 | 8ap6.37 | 8ap6.38 | 8ap6.39 | 8ap6.40 | 8ap6.41 | 8ap6.42 | 8ap6.43 | 8ap6.44 | 8ap6.45 | 8ap6.46 | 8ap6.47 | 8ap6.48 | 8ap6.49 | 8ap6.50 | 8ap6.51 | 8ap6.52 | 8ap6.53 | 8ap6.54 | 8ap6.55 | 8ap6.56 | 8ap6.57 | 8ap6.58 | 8ap6.59 | 8ap6.60 | 8ap6.61 | 8ap6.62 | 8ap6.63 | 8ap6.64 | 8ap6.65 | 8ap6.66 | 8ap6.67 | 8ap6.68 | 8ap6.69 | 8ap6.70 | 8ap6.71 | 8ap6.72 | 8ap6.73 | 8ap6.74 | 8ap6.75 | 8ap6.76 | 8ap6.77 | 8ap6.78 | 8ap6.79 | 8ap6.80 | 8ap7.1 | 8ap8.1 | 8ap9.1 | 8apa.1 | 8apb.1 | 8apc.1 | 8apd.1 | 8ape.1 | 8apf.1 | 8apg.1 | 8aph.1 | 8apj.1