Research workbench

Membrane arm of active state ci from rotenone-NADH dataset

Analyse Membrane arm of active state ci from rotenone-NADH dataset in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VC0
Type: protein
Length: 4,727 residues
Chains: 29
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial; NADH dehydrogenase…
EC: 7.1.1.2
UniProt: A0A480JYS1, K7GR43, A0A4X1VQ42, I3LGM4, F1S6Q1, D0G781, A0A4X1V766, A0A287AS93, F1SGC6, Q2EN80, F1RWL7, A0A4X1VYV0, A1XQS6, A0A480JRW3, F1SV23, O79875, O79880, P56632, Q71K68, O79882, F1SD73, A0A4X1T6M0, A0A4X1T0A8, Q7IIB7, O79874, F1SLR1, F1SCH1, F1SIS9
Ligands: CDL, PEE, PLX, MYR, 8Q1, UQ, ADP
Pockets: 20 · best druggability 0.91

Structure

electron microscopy · 29 distinct chains · 63% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Q	NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial	protein	44	23% helix, 2% strand	A0A480JYS1
S	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1	protein	70	59% helix, 0% strand	K7GR43
U	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3	protein	83	53% helix, 2% strand	A0A4X1VQ42
V	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11	protein	140	79% helix, 0% strand	I3LGM4
W	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13	protein	113	73% helix, 1% strand	F1S6Q1
X	Acyl carrier protein, mitochondrial	protein	88	49% helix, 0% strand	D0G781
Y	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial	protein	67	52% helix, 0% strand	A0A4X1V766
Z	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3	protein	80	55% helix, 0% strand	A0A287AS93
a	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial	protein	138	60% helix, 2% strand	F1SGC6
b	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6	protein	98	43% helix, 7% strand	Q2EN80
c	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial	protein	156	26% helix, 4% strand	F1RWL7
d	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10	protein	175	66% helix, 2% strand	A0A4X1VYV0
e	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial	protein	104	50% helix, 1% strand	—
f	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial	protein	49	67% helix, 0% strand	A1XQS6
g	NADH dehydrogenase [ubiquinone] 1 subunit C2	protein	122	57% helix, 2% strand	A0A480JRW3
h	NADH dehydrogenase [ubiquinone] iron-sulfur protein 5	protein	105	61% helix, 0% strand	F1SV23
i	NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2)	protein	347	75% helix, 2% strand	O79875
j	NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2)	protein	115	62% helix, 0% strand	O79880
k	NADH-ubiquinone oxidoreductase chain 4L (EC 7.1.1.2)	protein	98	81% helix, 2% strand	P56632
l	NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2)	protein	606	75% helix, 4% strand	Q71K68
m	NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2)	protein	175	68% helix, 0% strand	O79882
n	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1	protein	56	54% helix, 0% strand	F1SD73
o	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4	protein	128	62% helix, 1% strand	A0A4X1T6M0
p	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9	protein	178	56% helix, 0% strand	A0A4X1T0A8
r	NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2)	protein	459	74% helix, 2% strand	Q7IIB7
s	NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2)	protein	318	69% helix, 1% strand	O79874
u	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8	protein	171	46% helix, 2% strand	F1SLR1
v	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7	protein	124	59% helix, 1% strand	F1SCH1
w	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial	protein	320	53% helix, 8% strand	F1SIS9

Ligands and binding sites

CDL · Cardiolipin · ligand · 9 copies · chains V, i, l, a, b, d, e, r, k, m, c, p, o, g, n, w, s, u
PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 7 copies · chains Q, i, l, r, U, W, s, S, j, m, c, b, V
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 · ligand · 6 copies · chains a, e, l, r, g, h, i, j, m, n, V
MYR · Myristic acid · ligand · chains c, l, v
8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · chains X, l, p
UQ · Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer · ligand · chains s
ADP · Adenosine-5'-diphosphate · ligand · chains w

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1155	0.91	0.93	156	PEE
2	1063	0.87	0.89	107	empty
3	717	0.87	0.91	86	empty
4	1023	0.85	0.86	85	PEE
5	241	0.84	0.96	33	empty

Interfaces

121 interfaces between chains.

j–s · 3291 Å² buried · 16 hydrogen bonds · protein-protein
k–m · 2877 Å² buried · 16 hydrogen bonds · protein-protein
l–r · 2358 Å² buried · 13 hydrogen bonds · protein-protein
c–o · 2168 Å² buried · 37 hydrogen bonds · protein-protein
W–u · 1894 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 covalent, 1 lipid (disulfide, covalent ligand, myristoylation).

Compared structures

7VC0 · Membrane arm of active state CI from Rote -NADH dataset · the same entry in another collection · chain X against X, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A480JYS1
Every structure of UniProt K7GR43
Every structure of UniProt A0A4X1VQ42
Every structure of UniProt I3LGM4
Every structure of UniProt F1S6Q1
Every structure of UniProt D0G781
Every structure of UniProt A0A4X1V766
Every structure of UniProt A0A287AS93
Every structure of UniProt F1SGC6
Every structure of UniProt Q2EN80
Every structure of UniProt F1RWL7
Every structure of UniProt A0A4X1VYV0
Every structure of UniProt A1XQS6
Every structure of UniProt A0A480JRW3
Every structure of UniProt F1SV23
Every structure of UniProt O79875
Every structure of UniProt O79880
Every structure of UniProt P56632
Every structure of UniProt Q71K68
Every structure of UniProt O79882
Every structure of UniProt F1SD73
Every structure of UniProt A0A4X1T6M0
Every structure of UniProt A0A4X1T0A8
Every structure of UniProt Q7IIB7
Every structure of UniProt O79874
Every structure of UniProt F1SLR1
Every structure of UniProt F1SCH1
Every structure of UniProt F1SIS9
Elsewhere: RCSB PDB 7VC0 · PDBe 7VC0 · UniProt A0A480JYS1 · UniProt K7GR43 · UniProt A0A4X1VQ42 · UniProt I3LGM4 · UniProt F1S6Q1 · UniProt D0G781 · UniProt A0A4X1V766 · UniProt A0A287AS93 · UniProt F1SGC6 · UniProt Q2EN80 · UniProt F1RWL7 · UniProt A0A4X1VYV0 · UniProt A1XQS6 · UniProt A0A480JRW3 · UniProt F1SV23 · UniProt O79875 · UniProt O79880 · UniProt P56632 · UniProt Q71K68 · UniProt O79882 · UniProt F1SD73 · UniProt A0A4X1T6M0 · UniProt A0A4X1T0A8 · UniProt Q7IIB7 · UniProt O79874 · UniProt F1SLR1 · UniProt F1SCH1 · UniProt F1SIS9

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