MolNFT v1 · #113450 · protein

Cryo-EM structure of dynein tail-dynactin-BICD2N complex

5AFU: “Cryo-EM structure of dynein tail-dynactin-BICD2N complex”. Electron microscopy, 2 ligands (ADP, ATP), 20 pockets (best druggability 0.85). MolNFT v1 #113450 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5AFU
Type: protein
Length: 8,572 residues
Chains: 33
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dynein tail; Dynactin; Actin, cytoplasmic 1; Capping protein (actin filament) muscle…
UniProt: F2Z5G5, Q6QAQ1, I3LHK5, A0PFK5, D2JYW4
Ligands: ADP, ATP
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 22 distinct chains · 55% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Dynein tail	protein	361	70% helix, 2% strand	—
2	Dynein tail	protein	359	69% helix, 3% strand	—
3, 4	Dynein tail	protein	350	2% helix, 50% strand	—
5, 6	Dynein tail	protein	275	99% helix, 0% strand	—
A, B, C, D, E, F, G, I	Dynactin	protein	370	39% helix, 18% strand	F2Z5G5
H	Actin, cytoplasmic 1	protein	370	43% helix, 16% strand	Q6QAQ1
J	Dynactin	protein	369	40% helix, 13% strand	I3LHK5
K	Capping protein (actin filament) muscle Z-line, alpha 1	protein	275	38% helix, 31% strand	A0PFK5
L	F-actin capping protein beta subunit variant II	protein	270	42% helix, 31% strand	D2JYW4
M	Dynactin	protein	587	97% helix, 0% strand	—
N	Dynactin 6	protein	616	94% helix, 0% strand	—
O, P	Dynactin	protein	65	43% helix, 22% strand	—
Q, R	Dynactin	protein	87	93% helix, 0% strand	—
U	Dynactin	protein	168	15% helix, 30% strand	—
V	Dynactin	protein	165	11% helix, 25% strand	—
Y	F-actin-capping protein subunit beta	protein	243	10% helix, 12% strand	—
Z	F-actin-capping protein subunit beta	protein	52	67% helix, 0% strand	—
a	Dynactin	protein	48	19% helix, 8% strand	—
b	Dynactin	protein	71	13% helix, 6% strand	—
c	Dynactin	protein	31	0% helix, 19% strand	—
d	Dynactin	protein	20	0% helix, 15% strand	—
z	F-actin-capping protein subunit beta	protein	53	75% helix, 0% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 9 copies · chains A, B, C, D, E, F, G, I, J
ATP · Adenosine-5'-triphosphate · ligand · chains H

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	1127	0.85	0.86	114	empty
2	830	0.83	0.86	92	empty
3	716	0.83	0.86	78	ADP
4	1095	0.82	0.83	74	empty
5	1054	0.82	0.83	125	empty

Interfaces

70 interfaces between chains.

K–L · 3885 Å² buried · 39 hydrogen bonds · protein-protein
5–6 · 2422 Å² buried · 0 hydrogen bonds · protein-protein
G–b · 1624 Å² buried · 14 hydrogen bonds · protein-protein
J–Y · 1473 Å² buried · 11 hydrogen bonds · protein-protein
I–J · 1249 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

5AFU · Cryo-EM structure of dynein tail-dynactin-BICD2N complex · the same entry in another collection · chain d against d, 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 F2Z5G5
Every structure of UniProt Q6QAQ1
Every structure of UniProt I3LHK5
Every structure of UniProt A0PFK5
Every structure of UniProt D2JYW4
Elsewhere: RCSB PDB 5AFU · PDBe 5AFU · UniProt F2Z5G5 · UniProt Q6QAQ1 · UniProt I3LHK5 · UniProt A0PFK5 · UniProt D2JYW4

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