Research workbench

Plant mitochondrial respiratory complex I

Analyse Plant mitochondrial respiratory complex I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7A23
Type: protein
Length: 7,354 residues
Chains: 45
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 51KDA; NAD2M; NAD3M; NAD6M; NAD1M; NAD4LM; Pgiv; B16.6; Mwfe; B9; B14.5A; B14.5B; 15KDA…
Ligands: SF4, CDL, T7X, FES, FMN, U10, PEV, NDP, BCT, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 45 distinct chains · 46% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	51KDA	protein	429	43% helix, 10% strand	—
I	NAD2M	protein	481	72% helix, 1% strand	—
J	NAD3M	protein	96	73% helix, 0% strand	—
N	NAD6M	protein	149	58% helix, 0% strand	—
H	NAD1M	protein	318	59% helix, 0% strand	—
K	NAD4LM	protein	85	86% helix, 0% strand	—
Y	Pgiv	protein	98	71% helix, 0% strand	—
Z	B16.6	protein	140	44% helix, 1% strand	—
V	Mwfe	protein	57	70% helix, 0% strand	—
W	B9	protein	37	68% helix, 0% strand	—
S	B14.5A	protein	101	13% helix, 9% strand	—
i	B14.5B	protein	66	82% helix, 0% strand	—
j	15KDA	protein	68	69% helix, 0% strand	—
G	NAD7M	protein	382	45% helix, 9% strand	—
C	75KDA	protein	693	25% helix, 14% strand	—
T	39KDA	protein	328	32% helix, 11% strand	—
F	NAD9M	protein	178	12% helix, 17% strand	—
B	24KDA	protein	219	34% helix, 8% strand	—
O	18KDA	protein	111	14% helix, 15% strand	—
P	13KDA	protein	71	14% helix, 15% strand	—
R	B13	protein	129	48% helix, 4% strand	—
U	B17.2	protein	122	11% helix, 12% strand	—
E	Psst	protein	153	41% helix, 10% strand	—
D	Tyky	protein	177	38% helix, 16% strand	—
X	B14	protein	103	66% helix, 0% strand	—
c	20.9KDA	protein	99	54% helix, 0% strand	—
Q	B8	protein	92	33% helix, 18% strand	—
k	ACPM1	protein	78	47% helix, 3% strand	—
r	UNK1	protein	24	0% helix, 13% strand	—
n	P2	protein	27	67% helix, 0% strand	—
o	CAL1	protein	202	16% helix, 20% strand	—
q	CA1	protein	228	20% helix, 15% strand	—
p	CA1	protein	224	21% helix, 18% strand	—
M	NAD4M	protein	482	67% helix, 1% strand	—
f	Pdsw	protein	76	58% helix, 0% strand	—
g	Esss	protein	47	53% helix, 0% strand	—
d	B22	protein	66	68% helix, 0% strand	—
a	NAD5M	protein	600	62% helix, 1% strand	—
b	B18	protein	63	54% helix, 0% strand	—
h	Aggg	protein	28	82% helix, 0% strand	—
e	ACPM2	protein	84	52% helix, 0% strand	—
l	B15	protein	23	91% helix, 0% strand	—
s	UNK2	protein	20	90% helix, 0% strand	—
m	P1	protein	69	32% helix, 0% strand	—
t	B12-1	protein	31	81% helix, 0% strand	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, G, C, E, D
CDL · Cardiolipin · ligand · 3 copies · chains I, i, c, n, q, p, J, W, N
T7X · Phosphatidylinositol · ligand · 2 copies · chains I, i, c, n, q, p
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains C, A, B
FMN · Flavin mononucleotide · ligand · chains A
U10 · Ubiquinone-10 · ligand · chains H, E
PEV · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains H, Z, W, G, D
NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains T
BCT · Bicarbonate ion · ligand · chains q, p
ZN · Zinc ion · metal · 2 copies · chains P, q, p

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	668	0.88	0.91	98	empty
2	1181	0.87	0.88	126	empty
3	1166	0.86	0.87	144	NDP
4	704	0.85	0.88	62	U10
5	288	0.84	0.95	51	empty

Interfaces

156 interfaces between chains.

A–B · 3112 Å² buried · 41 hydrogen bonds · protein-protein
q–p · 2995 Å² buried · 28 hydrogen bonds · protein-protein
o–p · 2705 Å² buried · 33 hydrogen bonds · protein-protein
J–H · 2526 Å² buried · 9 hydrogen bonds · protein-protein
C–O · 2317 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

7A23 · Plant mitochondrial respiratory complex I · the same entry in another collection · chain I against I, 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
Elsewhere: RCSB PDB 7A23 · PDBe 7A23

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