Research workbench

Radial spoke 1 isolated from chlamydomonas reinhardtii

Analyse Radial spoke 1 isolated from chlamydomonas reinhardtii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JTK
Type: protein
Length: 9,516 residues
Chains: 39
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Flagellar radial spoke protein 1; Flagellar radial spoke protein 2; Flagellar radial…
EC: 1.-.-.-, 5.2.1.8, 2.7.4.6
UniProt: Q27YU0, Q6UBQ3, A8J2J7, A8I550, Q27YU7, Q01657, A0A2K3DL29, Q27YU5, Q27YU4, Q27YU3, A8I2U9, A8HNV0, A8IKR9, Q39580, Q69B19, A0A2K3DCN8, A0A2K3D359, A8JDM3
Ligands: PO4
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 23 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Flagellar radial spoke protein 1	protein	749	14% helix, 35% strand	Q27YU0
C, D	Flagellar radial spoke protein 2	protein	427	69% helix, 7% strand	Q6UBQ3
E	Flagellar radial spoke protein 3	protein	284	85% helix, 1% strand	A8J2J7
F	Flagellar radial spoke protein 3	protein	287	84% helix, 1% strand	A8J2J7
G, H	Flagellar radial spoke protein 4	protein	421	24% helix, 17% strand	A8I550
I, J	Flagellar radial spoke protein 5 (EC 1.-.-.-)	protein	483	46% helix, 10% strand	Q27YU7
K, L	Flagellar radial spoke protein 6	protein	428	23% helix, 15% strand	Q01657
M	Flagellar radial spoke protein 7	protein	47	60% helix, 0% strand	A0A2K3DL29
N	Flagellar radial spoke protein 7	protein	40	70% helix, 0% strand	A0A2K3DL29
O, P, Q, R	Flagellar radial spoke protein 9	protein	249	21% helix, 33% strand	Q27YU5
S, T	Flagellar radial spoke protein 10	protein	199	3% helix, 55% strand	Q27YU4
U	Flagellar radial spoke protein 11	protein	48	69% helix, 0% strand	Q27YU3
V	Flagellar radial spoke protein 11	protein	182	62% helix, 2% strand	Q27YU3
W	Flagellar radial spoke protein 12 (EC 5.2.1.8)	protein	163	16% helix, 31% strand	A8I2U9
X	Flagellar radial spoke protein 14	protein	379	69% helix, 0% strand	A8HNV0
Y, Z	Flagellar radial spoke protein 16	protein	213	17% helix, 37% strand	A8IKR9
a, b, c, d	Dynein 8 kda light chain, flagellar outer arm	protein	84	36% helix, 38% strand	Q39580
e	Unknown protein	protein	34	91% helix, 0% strand	—
i, j	Flagellar radial spoke protein 23 (EC 2.7.4.6)	protein	201	50% helix, 14% strand	Q69B19
k	Cytochrome B5 heme-binding domain-containing protein	protein	213	15% helix, 24% strand	A0A2K3DCN8
s	Uncharacterized protein	protein	37	0% helix, 30% strand	A0A2K3D359
u, v	Predicted protein	protein	50	82% helix, 0% strand	A8JDM3
y, z	Flagellar radial spoke protein 16	protein	64	64% helix, 0% strand	A8IKR9

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains G, H, K, L

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	1030	0.89	0.91	106	empty
2	1178	0.89	0.91	127	empty
3	1001	0.88	0.89	103	empty
4	792	0.87	0.90	124	empty
5	739	0.85	0.88	74	empty

Interfaces

131 interfaces between chains.

Y–Z · 2475 Å² buried · 8 hydrogen bonds · protein-protein
A–G · 2392 Å² buried · 22 hydrogen bonds · protein-protein
B–H · 2368 Å² buried · 22 hydrogen bonds · protein-protein
L–Q · 2156 Å² buried · 20 hydrogen bonds · protein-protein
K–O · 2136 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7JTK · Radial spoke 1 isolated from Chlamydomonas reinhardtii · the same entry in another collection · chain H against H, 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 Q27YU0
Every structure of UniProt Q6UBQ3
Every structure of UniProt A8J2J7
Every structure of UniProt A8I550
Every structure of UniProt Q27YU7
Every structure of UniProt Q01657
Every structure of UniProt A0A2K3DL29
Every structure of UniProt Q27YU5
Every structure of UniProt Q27YU4
Every structure of UniProt Q27YU3
Every structure of UniProt A8I2U9
Every structure of UniProt A8HNV0
Every structure of UniProt A8IKR9
Every structure of UniProt Q39580
Every structure of UniProt Q69B19
Every structure of UniProt A0A2K3DCN8
Every structure of UniProt A0A2K3D359
Every structure of UniProt A8JDM3
Elsewhere: RCSB PDB 7JTK · PDBe 7JTK · UniProt Q27YU0 · UniProt Q6UBQ3 · UniProt A8J2J7 · UniProt A8I550 · UniProt Q27YU7 · UniProt Q01657 · UniProt A0A2K3DL29 · UniProt Q27YU5 · UniProt Q27YU4 · UniProt Q27YU3 · UniProt A8I2U9 · UniProt A8HNV0 · UniProt A8IKR9 · UniProt Q39580 · UniProt Q69B19 · UniProt A0A2K3DCN8 · UniProt A0A2K3D359 · UniProt A8JDM3

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