Research workbench

Outer dynein arm-shulin complex - overall structure (tetrahymena thermophila)

Analyse Outer dynein arm-shulin complex - overall structure (tetrahymena thermophila) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZYW
Type: protein
Length: 15,675 residues
Chains: 19
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative; Outer arm…
UniProt: I7M6H4, I7M9J2, Q22A67, I7M008, Q23FU1, I7MHB1, Q22MV2, A4VE64, I7MCM8, Q24DI9, Q22R86, W7XJB1, Q24CE5, Q1HGH8, A4VEB3, Q240X9, Q22YU3
Ligands: ADP, ATP, GTP
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 19 distinct chains · 46% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dynein-1-alpha heavy chain, flagellar inner arm I1 complex protein, putative	protein	3795	48% helix, 9% strand	I7M6H4
B	Outer arm dynein beta heavy chain	protein	4370	54% helix, 5% strand	I7M9J2
C	Dynein heavy chain, outer arm protein	protein	4433	50% helix, 5% strand	Q22A67
D	Dynein intermediate chain 2	protein	321	3% helix, 39% strand	I7M008
E	Flagellar outer dynein arm intermediate protein, putative	protein	341	4% helix, 40% strand	Q23FU1
F	Dynein light chain roadblock-type 2 protein	protein	98	31% helix, 31% strand	I7MHB1
G	Dynein light chain roadblock-type 2 protein	protein	95	38% helix, 28% strand	Q22MV2
H	Dynein light chain	protein	85	38% helix, 39% strand	A4VE64
I	Dynein light chain	protein	89	37% helix, 37% strand	I7MCM8
J	Dynein light chain	protein	84	35% helix, 37% strand	Q24DI9
K	Dynein light chain	protein	95	34% helix, 32% strand	Q22R86
L	Dynein light chain	protein	97	30% helix, 36% strand	W7XJB1
M	Dynein light chain	protein	86	37% helix, 35% strand	Q24CE5
N	Dynein light chain 2A	protein	109	33% helix, 24% strand	Q1HGH8
O	Dynein light chain tctex-type 1 protein	protein	111	33% helix, 28% strand	A4VEB3
P	Thioredoxin	protein	103	35% helix, 25% strand	Q240X9
Y	Shulin	protein	1133	39% helix, 18% strand	Q22YU3
d	Dynein intermediate chain 2	protein	128	28% helix, 14% strand	I7M008
e	Flagellar outer dynein arm intermediate protein, putative	protein	102	21% helix, 14% strand	Q23FU1

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains C
ATP · Adenosine-5'-triphosphate · ligand · chains C
GTP · Guanosine-5'-triphosphate · ligand · chains Y

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	1082	0.82	0.83	126	empty
2	1131	0.82	0.83	147	empty
3	928	0.81	0.83	123	empty
4	953	0.81	0.83	98	empty
5	898	0.79	0.82	85	empty

Interfaces

37 interfaces between chains.

N–O · 679 Å² buried · 10 hydrogen bonds · protein-protein
L–M · 530 Å² buried · 16 hydrogen bonds · protein-protein
J–K · 435 Å² buried · 6 hydrogen bonds · protein-protein
N–d · 426 Å² buried · 7 hydrogen bonds · protein-protein
H–I · 417 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6ZYW · Outer Dynein Arm-Shulin complex - overall structure (Tetrahymena thermophila) · the same entry in another collection · chain L against L, 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 I7M6H4
Every structure of UniProt I7M9J2
Every structure of UniProt Q22A67
Every structure of UniProt I7M008
Every structure of UniProt Q23FU1
Every structure of UniProt I7MHB1
Every structure of UniProt Q22MV2
Every structure of UniProt A4VE64
Every structure of UniProt I7MCM8
Every structure of UniProt Q24DI9
Every structure of UniProt Q22R86
Every structure of UniProt W7XJB1
Every structure of UniProt Q24CE5
Every structure of UniProt Q1HGH8
Every structure of UniProt A4VEB3
Every structure of UniProt Q240X9
Every structure of UniProt Q22YU3
Elsewhere: RCSB PDB 6ZYW · PDBe 6ZYW · UniProt I7M6H4 · UniProt I7M9J2 · UniProt Q22A67 · UniProt I7M008 · UniProt Q23FU1 · UniProt I7MHB1 · UniProt Q22MV2 · UniProt A4VE64 · UniProt I7MCM8 · UniProt Q24DI9 · UniProt Q22R86 · UniProt W7XJB1 · UniProt Q24CE5 · UniProt Q1HGH8 · UniProt A4VEB3 · UniProt Q240X9 · UniProt Q22YU3

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