Research workbench

RS head-neck monomer

Analyse RS head-neck monomer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8WZB
Type: protein
Length: 2,181 residues
Chains: 11
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.28
Source: Mus musculus
Molecule: DPY30 domain containing 2; DnaJ homolog subfamily B member 13; Radial spoke head protein…
UniProt: Q9D3X8, Q80Y75, Q9DA80, Q99MH5, Q8VIG3, Q8BYM7, Q9D9V4
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · resolution 3.28 · 10 distinct chains · 27% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DPY30 domain containing 2	protein	46	80% helix, 0% strand	Q9D3X8
B	DnaJ homolog subfamily B member 13	protein	181	12% helix, 28% strand	Q80Y75
C	DnaJ homolog subfamily B member 13	protein	78	14% helix, 27% strand	Q80Y75
D	Radial spoke head protein 3 homolog B	protein	46	91% helix, 0% strand	Q9DA80
E	Nucleoside diphosphate kinase homolog 5	protein	201	46% helix, 13% strand	Q99MH5
F, I	Radial spoke head 1 homolog	protein	185	0% helix, 54% strand	Q8VIG3
G	Radial spoke head protein 4 homolog A	protein	387	27% helix, 17% strand	Q8BYM7
H	Radial spoke head protein 9 homolog	protein	239	23% helix, 26% strand	Q9D9V4
S	Radial spoke head protein 4 homolog A	protein	392	28% helix, 15% strand	Q8BYM7
c	Radial spoke head protein 9 homolog	protein	241	24% helix, 26% strand	Q9D9V4

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	445	0.86	0.93	56	empty
2	1080	0.85	0.86	126	empty
3	947	0.82	0.83	95	empty
4	661	0.81	0.86	80	empty
5	578	0.73	0.81	59	empty

Interfaces

26 interfaces between chains.

G–S · 2113 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 2036 Å² buried · 34 hydrogen bonds · protein-protein
S–I · 1902 Å² buried · 24 hydrogen bonds · protein-protein
F–G · 1868 Å² buried · 20 hydrogen bonds · protein-protein
S–c · 1700 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

Q9D9V4 · AlphaFold monomer V2.0 prediction for radial spoke head protein 9 homolog (Q9D9V4) · a predicted model of the same protein · chain c against A, TM-score 0.97
Q8VIG3 · AlphaFold monomer V2.0 prediction for radial spoke head 1 homolog (Q8VIG3) · a predicted model of the same protein · chain F against A, TM-score 0.94
Q9DA80 · AlphaFold monomer V2.0 prediction for radial spoke head protein 3 homolog B (Q9DA80) · a predicted model of the same protein · chain D against A, TM-score 0.93
Q80Y75 · AlphaFold monomer V2.0 prediction for dnaj homolog subfamily B member 13 (Q80Y75) · a predicted model of the same protein · chain B against A, TM-score 0.89
Q8BYM7 · AlphaFold monomer V2.0 prediction for radial spoke head protein 4 homolog a (Q8BYM7) · a predicted model of the same protein · chain G against A, TM-score 0.87
Q99MH5 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase homolog 5 (Q99MH5) · a predicted model of the same protein · chain E against A, TM-score 0.84

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 Q9D3X8
Every structure of UniProt Q80Y75
Every structure of UniProt Q9DA80
Every structure of UniProt Q99MH5
Every structure of UniProt Q8VIG3
Every structure of UniProt Q8BYM7
Every structure of UniProt Q9D9V4
Elsewhere: RCSB PDB 8WZB · PDBe 8WZB · UniProt Q9D3X8 · UniProt Q80Y75 · UniProt Q9DA80 · UniProt Q99MH5 · UniProt Q8VIG3 · UniProt Q8BYM7 · UniProt Q9D9V4

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