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Deactive state complex I from dq-NADH dataset

Analyse Deactive state complex I from dq-NADH dataset in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7V2K
Type: protein
Length: 8,174 residues
Chains: 45
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial; NADH dehydrogenase…
EC: 7.1.1.2
UniProt: F1RVN1, A0A287BDC0, I3LK43, A0A480VKQ8, F1RGE3, D0G781, A0A5G2RN85, A0A4X1VLA2, A0A480QJC4, A0A4X1TFI3, G8IFA6, F1SHD7, F1SQP4, A0A287BG40, A0A286ZNN4, A0A480JYS1, K7GR43, F1S031, A0A4X1VQ42, I3LGM4, F1S6Q1, A0A4X1V766, A0A287AS93, F1SGC6, Q2EN80, F1RWL7, A0A4X1VYV0, A1XQS6, A0A480JRW3, F1SV23, O79875, O79880, P56632, Q71K68, O79882, F1SD73, A0A4X1T6M0, A0A4X1T0A8, Q7IIB7, O79874, F1SLR1, F1SCH1, F1SIS9
Ligands: PEE, CDL, SF4, PLX, 8Q1, FES, FMN, NAI, NDP, UQ, ADP, MG, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 44 distinct chains · 53% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 7.1.1.2)	protein	431	47% helix, 14% strand	F1RVN1
B	NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial	protein	176	37% helix, 17% strand	A0A287BDC0
C	NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial	protein	156	49% helix, 13% strand	I3LK43
E	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6	protein	115	61% helix, 0% strand	A0A480VKQ8
F	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	protein	86	42% helix, 27% strand	F1RGE3
G, X	Acyl carrier protein, mitochondrial	protein	88	58% helix, 0% strand	D0G781
H	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5	protein	112	56% helix, 0% strand	A0A5G2RN85
I	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7	protein	97	25% helix, 4% strand	A0A4X1VLA2
J	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial	protein	331	43% helix, 16% strand	A0A480QJC4
K	NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial	protein	42	40% helix, 0% strand	A0A4X1TFI3
L	NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial	protein	125	14% helix, 18% strand	G8IFA6
M	NADH-ubiquinone oxidoreductase 75 kda subunit, mitochondrial	protein	690	34% helix, 17% strand	F1SHD7
N	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12	protein	144	24% helix, 11% strand	F1SQP4
O	NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial	protein	217	38% helix, 11% strand	A0A287BG40
P	NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial	protein	208	22% helix, 26% strand	A0A286ZNN4
Q	NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial	protein	419	49% helix, 13% strand	A0A480JYS1
S	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1	protein	70	64% helix, 0% strand	K7GR43
T	NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial	protein	96	16% helix, 20% strand	F1S031
U	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3	protein	83	52% 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	142	58% helix, 1% strand	F1S6Q1
Y	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial	protein	70	44% helix, 0% strand	A0A4X1V766
Z	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3	protein	84	49% helix, 0% strand	A0A287AS93
a	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial	protein	140	59% helix, 3% strand	F1SGC6
b	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6	protein	103	45% helix, 6% strand	Q2EN80
c	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial	protein	156	28% helix, 4% strand	F1RWL7
d	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10	protein	175	66% helix, 3% strand	A0A4X1VYV0
e	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial	protein	107	46% helix, 1% strand	—
f	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial	protein	42	79% helix, 0% strand	A1XQS6
g	NADH dehydrogenase [ubiquinone] 1 subunit C2	protein	121	58% helix, 2% strand	A0A480JRW3
h	NADH dehydrogenase [ubiquinone] iron-sulfur protein 5	protein	105	60% helix, 0% strand	F1SV23
i	NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2)	protein	347	74% helix, 2% strand	O79875
j	NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2)	protein	99	73% helix, 0% strand	O79880
k	NADH-ubiquinone oxidoreductase chain 4L (EC 7.1.1.2)	protein	98	80% helix, 0% strand	P56632
l	NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2)	protein	603	75% helix, 4% strand	Q71K68
m	NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2)	protein	129	72% helix, 0% strand	O79882
n	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1	protein	56	45% helix, 0% strand	F1SD73
o	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4	protein	128	64% helix, 0% strand	A0A4X1T6M0
p	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9	protein	178	54% helix, 0% strand	A0A4X1T0A8
r	NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2)	protein	459	75% helix, 2% strand	Q7IIB7
s	NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2)	protein	303	69% helix, 1% strand	O79874
u	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8	protein	171	47% helix, 2% strand	F1SLR1
v	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7	protein	124	61% helix, 1% strand	F1SCH1
w	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial	protein	320	49% helix, 8% strand	F1SIS9

Ligands and binding sites

PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 8 copies · chains C, J, j, s, U, V, i, r, Q, l, c, b, S, W, m, B
CDL · Cardiolipin · ligand · 7 copies · chains B, I, N, S, s, a, b, d, e, l, r, i, w, c, g, n, u
SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B, C, Q, M
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 B, C, N, s, V, r, a, e, l, g, h, i, j, m, n
8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · 2 copies · chains E, G, X, l, p
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains M, A, O
FMN · Flavin mononucleotide · ligand · chains A
NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A
NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains C, J
UQ · Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer · ligand · chains C, s
ADP · Adenosine-5'-diphosphate · ligand · chains w
MG · Magnesium ion · metal · chains M
ZN · Zinc ion · metal · chains T

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	649	0.88	0.93	107	empty
2	581	0.88	0.93	84	PEE
3	981	0.88	0.89	105	PEE, NDP
4	1084	0.87	0.88	85	empty
5	543	0.87	0.93	84	empty

Interfaces

202 interfaces between chains.

A–O · 3265 Å² buried · 41 hydrogen bonds · protein-protein
P–Q · 2730 Å² buried · 33 hydrogen bonds · protein-protein
j–s · 2670 Å² buried · 9 hydrogen bonds · protein-protein
l–r · 2378 Å² buried · 11 hydrogen bonds · protein-protein
k–m · 2375 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 4 covalent, 1 modified (disulfide, covalent ligand, methylation).

Compared structures

7V2K · Deactive state complex I from DQ-NADH dataset · the same entry in another collection · chain l against l, TM-score 1.00

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