- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer
- Ligands
- 8 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)
- 8 x CDL: CARDIOLIPIN(Non-covalent)
CDL.3: 20 residues within 4Å:- Chain D: I.27, T.31, I.34, V.35, Y.38, S.39, L.42, K.43, Y.58, I.65, G.66, F.69
- Chain Q: M.157, L.160, I.164
- Chain T: M.576, V.577, Q.580, I.597
- Ligands: PEE.2
16 PLIP interactions:11 interactions with chain D, 2 interactions with chain Q, 3 interactions with chain T- Hydrophobic interactions: D:I.27, D:T.31, D:I.34, D:V.35, D:V.35, D:Y.38, D:Y.38, D:L.42, D:I.65, D:F.69, Q:L.160, Q:I.164, T:V.577, T:I.597
- Hydrogen bonds: D:Y.58, T:Q.580
CDL.5: 26 residues within 4Å:- Chain I: L.27, V.33, A.34, T.38, N.41, V.42, E.46, H.66
- Chain J: W.79, I.80, I.81, Y.83, H.88
- Chain L: R.42, P.43, A.47, R.48, H.55
- Chain M: V.53, S.56, A.60, Y.61
- Chain T: T.13, F.80
- Ligands: PEE.7, PLX.18
18 PLIP interactions:5 interactions with chain I, 2 interactions with chain M, 3 interactions with chain L, 7 interactions with chain J, 1 interactions with chain T- Hydrophobic interactions: I:L.27, I:V.33, M:V.53, L:P.43, L:A.47, J:W.79, J:W.79, J:I.80, J:Y.83, J:Y.83, J:Y.83, T:F.80
- Hydrogen bonds: I:N.41, I:E.46, M:Y.61, L:R.48
- Salt bridges: I:H.66, J:H.88
CDL.9: 33 residues within 4Å:- Chain 2: Y.304
- Chain O: F.37, C.41, L.44, I.45, A.48, V.54, V.55
- Chain Q: P.238, V.239, S.242, L.243, M.245, V.246, T.334, L.335
- Chain V: W.10
- Chain Y: M.10, L.12, P.13, W.16, M.17, T.90, R.91, L.94, T.97, M.98, L.101, F.105, V.127, I.131, R.135
- Ligands: CDL.22
29 PLIP interactions:12 interactions with chain Y, 9 interactions with chain O, 5 interactions with chain Q, 2 interactions with chain 2, 1 interactions with chain V- Hydrophobic interactions: Y:L.12, Y:P.13, Y:W.16, Y:L.94, Y:T.97, Y:L.101, Y:F.105, Y:V.127, Y:I.131, Y:I.131, Y:R.135, O:F.37, O:L.44, O:L.44, O:I.45, O:A.48, O:V.54, O:V.54, O:V.55, Q:V.239, Q:L.243, Q:V.246, Q:T.334, Q:L.335, V:W.10
- Hydrogen bonds: Y:T.90, O:V.54, 2:Y.304
- Salt bridges: 2:K.303
CDL.10: 19 residues within 4Å:- Chain 2: P.5, V.9
- Chain Q: P.3, Y.6, T.7, T.8, I.10, M.11, M.14, K.46, Q.125, L.128, L.129, T.132, W.133, L.213, K.321, M.323, L.325
10 PLIP interactions:10 interactions with chain Q- Hydrophobic interactions: Q:Y.6, Q:L.128, Q:L.129, Q:W.133, Q:W.133, Q:L.213, Q:L.325
- Hydrogen bonds: Q:Q.125
- Salt bridges: Q:K.46, Q:K.321
CDL.13: 25 residues within 4Å:- Chain I: L.19
- Chain T: I.19, M.20, S.22, N.23, L.78, R.116, K.119, Y.120, L.123, I.130, I.142, G.146, L.153
- Chain Y: P.353, L.354, T.357, V.361, L.369, P.371, S.372, L.445, T.448
- Ligands: PEE.7, PLX.18
13 PLIP interactions:4 interactions with chain Y, 9 interactions with chain T- Hydrophobic interactions: Y:V.361, Y:T.448, T:L.78, T:L.123, T:I.142, T:L.153
- Hydrogen bonds: Y:T.357, Y:T.357, T:Y.120
- Salt bridges: T:R.116, T:K.119, T:K.119, T:K.119
CDL.14: 23 residues within 4Å:- Chain K: G.105, F.109
- Chain T: L.286, I.293, T.294, L.410, M.411, L.413, I.414, S.417, L.418, A.421, R.425, F.429, V.493, M.496, L.500, L.504, K.514, P.516, S.517, T.519, Y.520
22 PLIP interactions:19 interactions with chain T, 3 interactions with chain K- Hydrophobic interactions: T:L.286, T:I.293, T:I.293, T:L.410, T:L.413, T:I.414, T:L.418, T:A.421, T:V.493, T:L.500, T:L.500, T:L.504, T:T.519, K:F.109, K:F.109, K:F.109
- Hydrogen bonds: T:S.517, T:S.517, T:Y.520, T:Y.520
- Salt bridges: T:R.425, T:K.514
CDL.16: 15 residues within 4Å:- Chain D: Y.107, G.108
- Chain T: W.557, L.558
- Chain W: P.81, T.82, P.83, S.86, L.87, G.89, A.90, G.93, I.94, L.97
- Chain Y: L.264
10 PLIP interactions:4 interactions with chain W, 1 interactions with chain Y, 2 interactions with chain D, 3 interactions with chain T- Hydrophobic interactions: W:L.87, W:A.90, W:I.94, W:L.97, Y:L.264, T:W.557, T:W.557, T:L.558
- Hydrogen bonds: D:Y.107, D:G.108
CDL.22: 23 residues within 4Å:- Chain 0: F.168, W.169, T.170, M.171
- Chain O: T.28, P.30, R.31, V.33, Y.34, F.37
- Chain Q: P.256, L.335, P.338
- Chain V: F.21, L.25, R.28, S.29
- Chain Y: L.2, I.5, I.6, T.9, F.56
- Ligands: CDL.9
15 PLIP interactions:4 interactions with chain Y, 2 interactions with chain O, 3 interactions with chain 0, 3 interactions with chain Q, 3 interactions with chain V- Hydrophobic interactions: Y:L.2, Y:I.5, Y:I.6, Y:F.56, O:V.33, O:F.37, 0:F.168, Q:P.256, Q:L.335, Q:P.338, V:F.21, V:L.25
- Hydrogen bonds: 0:T.170, 0:T.170
- Salt bridges: V:R.28
- 1 x 8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate(Covalent)
8Q1.4: 17 residues within 4Å:- Chain F: S.44, L.45
- Chain T: Y.515
- Chain X: H.11, Q.12, R.46, F.47, H.50, K.51, E.53, A.59, L.62, L.63, A.66, E.69, F.70, G.73
5 PLIP interactions:2 interactions with chain F, 3 interactions with chain X- Hydrogen bonds: F:S.44, F:L.45, X:A.59
- Hydrophobic interactions: X:K.51, X:A.66
- 4 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)
PLX.6: 13 residues within 4Å:- Chain I: H.60, R.74, T.75, F.76, Y.77, D.78
- Chain M: T.57, F.58
- Chain V: F.19, C.23
- Chain Y: K.3, L.36, S.40
12 PLIP interactions:2 interactions with chain I, 1 interactions with chain V, 6 interactions with chain Y, 3 interactions with chain M- Hydrophobic interactions: I:F.76, V:F.19, Y:K.3, Y:L.36, Y:L.36, M:T.57, M:F.58, M:F.58
- Salt bridges: I:D.78, Y:K.3
- Hydrogen bonds: Y:S.40, Y:S.40
PLX.8: 23 residues within 4Å:- Chain O: S.4, R.9, P.11, L.12, Q.13, F.14, M.35, F.72, L.76, R.79
- Chain P: P.1, F.2, F.3
- Chain Q: I.202, L.203, L.206, I.207, T.210, L.332, M.339, A.342, L.346, N.347
14 PLIP interactions:8 interactions with chain Q, 6 interactions with chain O- Hydrophobic interactions: Q:L.203, Q:L.206, Q:I.207, Q:L.332, Q:L.332, Q:L.332, Q:M.339, Q:A.342, O:F.72, O:F.72, O:F.72, O:L.76
- Salt bridges: O:R.9, O:R.79
PLX.12: 10 residues within 4Å:- Chain R: N.83, T.86, M.90, F.93
- Chain U: S.148, Y.149, T.151, W.152, I.155, W.159
6 PLIP interactions:4 interactions with chain U, 2 interactions with chain R- Hydrophobic interactions: U:T.151, U:W.152, U:W.159, R:F.93
- pi-Cation interactions: U:Y.149
- Hydrogen bonds: R:T.86
PLX.18: 16 residues within 4Å:- Chain M: S.56, V.59, A.60, Y.61
- Chain T: M.20, W.66
- Chain Y: V.67, L.68, W.71, P.443, L.446, L.447, N.450
- Ligands: CDL.5, PEE.7, CDL.13
6 PLIP interactions:1 interactions with chain M, 5 interactions with chain Y- Hydrophobic interactions: M:V.59, Y:W.71, Y:W.71, Y:P.443, Y:L.446
- Hydrogen bonds: Y:N.450
- 1 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)
UQ.21: 12 residues within 4Å:- Chain Z: L.14, L.15, A.18, T.21, R.25, D.51, A.52, L.55, F.56, F.220, F.224, M.225
12 PLIP interactions:12 interactions with chain Z- Hydrophobic interactions: Z:L.15, Z:A.18, Z:D.51, Z:A.52, Z:F.56, Z:F.56, Z:F.220, Z:F.224, Z:F.224
- Hydrogen bonds: Z:T.21, Z:R.25
- pi-Stacking: Z:F.224
- 1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.23: 12 residues within 4Å:- Chain 2: I.31, C.32, E.53, L.79, Y.83, Q.97, L.100, R.104, R.126, F.134, M.138, E.191
15 PLIP interactions:15 interactions with chain 2- Hydrogen bonds: 2:C.32, 2:E.53, 2:Y.83, 2:Y.83, 2:Q.97, 2:Q.97, 2:R.104, 2:R.104, 2:E.191, 2:E.191
- Salt bridges: 2:K.35, 2:K.35, 2:R.126
- pi-Stacking: 2:F.134, 2:F.134
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gu, J. et al., The coupling mechanism of mammalian mitochondrial complex I. Nat.Struct.Mol.Biol. (2022)
- Release Date
- 2022-12-14
- Peptides
- NADH dehydrogenase [ubiquinone] iron-sulfur protein 2: A
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1: B
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3: C
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11: D
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13: E
Acyl carrier protein: F
NADH-ubiquinone oxidoreductase AGGG subunit: G
NADH-ubiquinone oxidoreductase B12 subunit: H
NADH-ubiquinone oxidoreductase SGDH subunit: I
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6: J
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial: K
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10: L
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial: M
NADH-ubiquinone oxidoreductase KFYI subunit: N
NADH dehydrogenase [ubiquinone] 1 subunit C2: O
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5: P
NADH-ubiquinone oxidoreductase chain 2: Q
NADH-ubiquinone oxidoreductase chain 3: R
NADH-ubiquinone oxidoreductase chain 4L: S
NADH-ubiquinone oxidoreductase chain 5: T
NADH-ubiquinone oxidoreductase chain 6: U
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1: V
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4: W
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9: X
NADH-ubiquinone oxidoreductase chain 4: Y
NADH-ubiquinone oxidoreductase chain 1: Z
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8: 0
NADH-ubiquinone oxidoreductase B18 subunit: 1
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial: 2 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
QB
SC
UD
VE
WF
XG
YH
ZI
aJ
bK
cL
dM
eN
fO
gP
hQ
iR
jS
kT
lU
mV
nW
oX
pY
rZ
s0
u1
v2
w - Membrane
-
We predict this structure to be a membrane protein.
SMTL ID : 7vye.1
Membrane arm of deactive state CI from Q10-NADH dataset
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Acyl carrier protein
NADH-ubiquinone oxidoreductase AGGG subunit
NADH-ubiquinone oxidoreductase B12 subunit
NADH-ubiquinone oxidoreductase SGDH subunit
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
NADH-ubiquinone oxidoreductase KFYI subunit
NADH dehydrogenase [ubiquinone] 1 subunit C2
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
NADH-ubiquinone oxidoreductase chain 2
NADH-ubiquinone oxidoreductase chain 3
NADH-ubiquinone oxidoreductase chain 4L
NADH-ubiquinone oxidoreductase chain 5
NADH-ubiquinone oxidoreductase chain 6
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
NADH-ubiquinone oxidoreductase chain 4
NADH-ubiquinone oxidoreductase chain 1
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
NADH-ubiquinone oxidoreductase B18 subunit
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Related Entries With Identical Sequence
5gpn.30 | 5gpn.31 | 5gpn.34 | 5gpn.36 | 5gpn.63 | 5gup.18 | 5gup.34 | 5gup.36 | 5gup.38 | 5gup.43 | 7v2c.1 | 7v2d.1 | 7v2e.1 | 7v2f.1 | 7v2h.1 | 7v2k.1 | 7v2r.1 | 7v30.1 | 7v31.1 | 7v32.1 | 7v33.1 | 7v3m.1 | 7vb7.1 | 7vbl.1 | 7vbn.1 | 7vbp.1 | 7vbz.1 | 7vc0.1 | 7vwj.1 | 7vwl.1 more...less...7vxp.1 | 7vxs.1 | 7vy1.1 | 7vy8.1 | 7vy9.1 | 7vya.1 | 7vyf.1 | 7vyg.1 | 7vyh.1 | 7vyi.1 | 7vyn.1 | 7vys.1 | 7vz1.1 | 7vz8.1 | 7vzv.1 | 7vzw.1 | 7w00.1 | 7w0h.1 | 7w0r.1 | 7w0y.1 | 7w1o.1 | 7w1p.1 | 7w1t.1 | 7w1u.1 | 7w1v.1 | 7w1z.1 | 7w20.1 | 7w2k.1 | 7w2l.1 | 7w2r.1 | 7w2u.1 | 7w2y.1 | 7w31.1 | 7w32.1 | 7w35.1 | 7w4c.1 | 7w4d.1 | 7w4e.1 | 7w4f.1 | 7w4g.1 | 7w4j.1 | 7w4k.1 | 7w4l.1 | 7w4m.1 | 7w4n.1 | 7w4q.1 | 8ud1.1 | 8ueo.1 | 8uep.1 | 8ueq.1 | 8uer.1 | 8ues.1 | 8uet.1 | 8ueu.1 | 8uev.1 | 8uew.1 | 8uex.1 | 8uey.1 | 8uez.1 | 8ugh.10 | 8ugh.11 | 8ugh.14 | 8ugi.10 | 8ugi.11 | 8ugi.14 | 8ugj.10 | 8ugj.11 | 8ugj.14 | 8ugn.10 | 8ugn.11 | 8ugn.14 | 8ugn.91 | 8ugn.92 | 8ugn.95 | 8ugr.10 | 8ugr.11 | 8ugr.14 | 8ugr.91 | 8ugr.92 | 8ugr.95