Research workbench

Deactive state complex I from rotenone-NADH dataset

Analyse Deactive state complex I 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: 7V3M
Type: protein
Length: 8,140 residues
Chains: 45
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
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

Structure

electron microscopy · 44 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	431	—	F1RVN1
B	—	protein	176	—	A0A287BDC0
C	—	protein	156	—	I3LK43
E	—	protein	115	—	A0A480VKQ8
F	—	protein	86	—	F1RGE3
G, X	—	protein	88	—	D0G781
H	—	protein	112	—	A0A5G2RN85
I	—	protein	97	—	A0A4X1VLA2
J	—	protein	297	—	A0A480QJC4
K	—	protein	42	—	A0A4X1TFI3
L	—	protein	125	—	G8IFA6
M	—	protein	690	—	F1SHD7
N	—	protein	144	—	F1SQP4
O	—	protein	217	—	A0A287BG40
P	—	protein	208	—	A0A286ZNN4
Q	—	protein	419	—	A0A480JYS1
S	—	protein	70	—	K7GR43
T	—	protein	96	—	F1S031
U	—	protein	83	—	A0A4X1VQ42
V	—	protein	140	—	I3LGM4
W	—	protein	142	—	F1S6Q1
Y	—	protein	70	—	A0A4X1V766
Z	—	protein	84	—	A0A287AS93
a	—	protein	140	—	F1SGC6
b	—	protein	103	—	Q2EN80
c	—	protein	156	—	F1RWL7
d	—	protein	175	—	A0A4X1VYV0
e	—	protein	107	—	—
f	—	protein	42	—	A1XQS6
g	—	protein	121	—	A0A480JRW3
h	—	protein	105	—	F1SV23
i	—	protein	347	—	O79875
j	—	protein	99	—	O79880
k	—	protein	98	—	P56632
l	—	protein	603	—	Q71K68
m	—	protein	129	—	O79882
n	—	protein	56	—	F1SD73
o	—	protein	128	—	A0A4X1T6M0
p	—	protein	178	—	A0A4X1T0A8
r	—	protein	459	—	Q7IIB7
s	—	protein	303	—	O79874
u	—	protein	171	—	F1SLR1
v	—	protein	124	—	F1SCH1
w	—	protein	320	—	F1SIS9

Ligands and binding sites

PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 8 copies · chains B, Q, U, W, s, C, J, j, i, l, r, S, m, c, b, V
CDL · Cardiolipin · ligand · 7 copies · chains 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, a, e, n, r, g, h, i, j, m, l
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, p
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains M, 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.

Compared structures

7V3M · Deactive state complex I from rote -NADH dataset · the same entry in another collection · chain L against L, TM-score 1.00

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