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Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2

Analyse Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NW4
Type: protein
Length: 10,707 residues
Chains: 39
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dynein heavy chain; Dynein intermediate chain; Dynein N-terminal dimerization domain…
UniProt: F2Z5G5, I3LVD5, I3LHK5, A0PFK5, D2JYW4, D0G6S1, A0A0J9X292, A0A0J9X293, A0A0J9X299
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 28 distinct chains · 57% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Dynein heavy chain	protein	889	86% helix, 0% strand	—
D	Dynein intermediate chain	protein	341	2% helix, 51% strand	—
C	Dynein intermediate chain	protein	350	2% helix, 51% strand	—
A	Dynein heavy chain	protein	922	86% helix, 0% strand	—
1	Dynein N-terminal dimerization domain	protein	125	62% helix, 6% strand	—
2	Dynein N-terminal dimerization domain	protein	124	65% helix, 8% strand	—
R, S	Robl	protein	120	45% helix, 29% strand	—
E	Dynein light intermediate chain	protein	295	39% helix, 15% strand	—
F	Dynein light intermediate chain	protein	298	41% helix, 17% strand	—
G, H, O, P, Q, T, U, W	ARP1	protein	370	39% helix, 18% strand	F2Z5G5
V	Beta-actin	protein	370	43% helix, 16% strand	I3LVD5
X	ARP11	protein	369	40% helix, 13% strand	I3LHK5
Y	Capping protein (actin filament) muscle Z-line, alpha 1	protein	275	38% helix, 31% strand	A0PFK5
Z	F-actin capping protein beta subunit variant II	protein	270	42% helix, 31% strand	D2JYW4
a	Dynactin shoulder complex	protein	571	93% helix, 0% strand	—
b	Dynactin shoulder complex	protein	602	90% helix, 0% strand	—
c, d	Dynactin shoulder complex	protein	65	43% helix, 22% strand	—
e, f	Dynactin shoulder complex	protein	87	93% helix, 0% strand	—
g	Dynactin 6	protein	169	13% helix, 30% strand	D0G6S1
h	Dynactin subunit 5	protein	165	11% helix, 25% strand	—
i	Dynactin pointed end P62	protein	243	10% helix, 12% strand	—
j	P150	protein	52	67% helix, 0% strand	—
k	Dynactin	protein	48	19% helix, 8% strand	A0A0J9X292
l	Dynactin	protein	71	13% helix, 8% strand	A0A0J9X293
m	Dynactin	protein	31	0% helix, 19% strand	A0A0J9X299
n	Dynactin	protein	20	0% helix, 15% strand	—
o	Dynactin P150	protein	53	75% helix, 0% strand	—
5, 6	BICD2N	protein	275	99% helix, 0% strand	—

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	964	0.84	0.85	100	empty
2	574	0.83	0.88	75	empty
3	746	0.83	0.86	98	empty
4	809	0.83	0.86	90	empty
5	1136	0.82	0.84	85	empty

Interfaces

76 interfaces between chains.

Y–Z · 3889 Å² buried · 39 hydrogen bonds · protein-protein
5–6 · 2410 Å² buried · 0 hydrogen bonds · protein-protein
U–l · 1592 Å² buried · 15 hydrogen bonds · protein-protein
X–i · 1473 Å² buried · 11 hydrogen bonds · protein-protein
W–X · 1382 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5NW4 · Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2 · 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 I3LVD5
Every structure of UniProt I3LHK5
Every structure of UniProt A0PFK5
Every structure of UniProt D2JYW4
Every structure of UniProt D0G6S1
Every structure of UniProt A0A0J9X292
Every structure of UniProt A0A0J9X293
Every structure of UniProt A0A0J9X299
Elsewhere: RCSB PDB 5NW4 · PDBe 5NW4 · UniProt F2Z5G5 · UniProt I3LVD5 · UniProt I3LHK5 · UniProt A0PFK5 · UniProt D2JYW4 · UniProt D0G6S1 · UniProt A0A0J9X292 · UniProt A0A0J9X293 · UniProt A0A0J9X299

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