Research workbench

Cryo-EM structure of polytomella complex-I (membrane arm)

Analyse Cryo-EM structure of polytomella complex-I (membrane arm) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AR9
Type: protein
Length: 5,291 residues
Chains: 35
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ND3; ND1; ND6; ND4L; ND5; ND4; ND2; C1-fdx; SDAP1; Pgiv; B14.7; B16.6; Mwfe; B9; Kfyi…
Ligands: PC7, PTY, CDL, 8Q1
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 35 distinct chains · 59% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ND3	protein	121	63% helix, 0% strand	—
H	ND1	protein	293	74% helix, 1% strand	—
J	ND6	protein	145	74% helix, 0% strand	—
K	ND4L	protein	104	78% helix, 0% strand	—
L	ND5	protein	536	75% helix, 5% strand	—
M	ND4	protein	438	72% helix, 3% strand	—
N	ND2	protein	375	78% helix, 0% strand	—
O	C1-fdx	protein	161	24% helix, 22% strand	—
T	SDAP1	protein	83	57% helix, 2% strand	—
X	Pgiv	protein	99	74% helix, 1% strand	—
Y	B14.7	protein	205	55% helix, 3% strand	—
Z	B16.6	protein	124	53% helix, 0% strand	—
a	Mwfe	protein	60	80% helix, 0% strand	—
b	B9	protein	54	72% helix, 0% strand	—
c	Kfyi	protein	97	35% helix, 6% strand	—
d	B14.5B	protein	80	76% helix, 1% strand	—
e	15 kda	protein	71	72% helix, 3% strand	—
f	Mnll	protein	111	59% helix, 3% strand	—
g	Esss	protein	147	61% helix, 1% strand	—
h	NUOP4	protein	77	64% helix, 1% strand	—
i	NUOP5	protein	111	44% helix, 11% strand	—
j	Aggg	protein	87	46% helix, 8% strand	—
k	B12	protein	44	68% helix, 0% strand	—
l	Ashi	protein	127	41% helix, 6% strand	—
m	B15	protein	111	43% helix, 5% strand	—
n	B22	protein	120	51% helix, 3% strand	—
o	B18	protein	83	65% helix, 0% strand	—
p	Pdsw	protein	155	65% helix, 3% strand	—
s	NUOP7	protein	115	47% helix, 2% strand	—
t	NUOP8	protein	82	62% helix, 0% strand	—
u	Unknown	protein	50	96% helix, 0% strand	—
w	Unknown	protein	41	78% helix, 2% strand	—
x	Cal	protein	250	23% helix, 27% strand	—
y	CA2	protein	308	28% helix, 26% strand	—
z	CA3	protein	226	30% helix, 29% strand	—

Ligands and binding sites

PC7 · (7S)-4-hydroxy-N,N,N-trimethyl-9-oxo-7-[(palmitoyloxy) methyl]-3,5,8-trioxa-4-phosphahexacosan-1-aminium 4-oxide · ligand · 7 copies · chains A, H, N, b, y, L, M, c, n, h, l, g, d, f, J, z
PTY · Phosphatidylethanolamine · ligand · 7 copies · chains H, Z, b, L, h, l, M, Y, g, N, O, m
CDL · Cardiolipin · ligand · 5 copies · chains L, M, Y, m, s, t, N, d, n, f, i, y, z
8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · chains T, n, s

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	983	0.89	0.91	140	empty
2	945	0.88	0.90	102	PC7
3	1196	0.85	0.86	98	empty
4	744	0.85	0.88	61	empty
5	356	0.84	0.93	45	empty

Interfaces

158 interfaces between chains.

x–y · 3547 Å² buried · 45 hydrogen bonds · protein-protein
J–K · 3207 Å² buried · 20 hydrogen bonds · protein-protein
y–z · 2708 Å² buried · 23 hydrogen bonds · protein-protein
A–H · 2568 Å² buried · 4 hydrogen bonds · protein-protein
L–l · 2466 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7AR9 · Cryo-EM structure of Polytomella Complex-I (membrane arm) · the same entry in another collection · chain H against H, 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 7AR9 · PDBe 7AR9

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