MolNFT v1 · #82361 · protein

X-ray structure of a functional full-length dynein motor domain

3VKH · Dynein heavy chain, cytoplasmic: “X-ray structure of a functional full-length dynein motor domain”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.84). MolNFT v1 #82361 on GenesisL1: 3D structure, binding sites…

PDB: 3VKH
Type: protein
Length: 5,950 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dynein heavy chain, cytoplasmic
UniProt: P34036
Ligands: ADP
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 55% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dynein heavy chain, cytoplasmic	protein	3042	55% helix, 8% strand	P34036
B	Dynein heavy chain, cytoplasmic	protein	2908	55% helix, 9% strand	P34036

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B

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	1200	0.84	0.85	132	ADP
2	1027	0.81	0.82	104	ADP
3	539	0.81	0.87	53	empty
4	820	0.78	0.81	99	empty
5	815	0.77	0.81	70	empty

Interfaces

1 interface between chains.

A–B · 1328 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

3VKH · X-ray structure of a functional full-length dynein motor domain · the same entry in another collection · chain B against B, 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 P34036
Elsewhere: RCSB PDB 3VKH · PDBe 3VKH · UniProt P34036

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