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7E80: Cryo-EM structure of the flagellar rod with hook and export apparatus from Salmonella

Analyse 7E80: Cryo-EM structure of the flagellar rod with hook and export apparatus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7E80
Type: protein
Length: 15,371 residues
Chains: 77
Method: electron microscopy
Authors: Tan, J.X., Chang, S.H., Wang, X.F., Xu, C.H., Zhou, Y., Zhang, X., Zhu, Y.Q.
Deposited: 02/28/21
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.67
Source: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Molecule: Flagellar basal-body rod protein FlgG; Flagellar basal-body rod protein FlgF; Flagellar…
UniProt: P0A1J3, P16323, P15928, P0A1I7, P16437, P26462, P0A1J1, P54702, P0A1L5, P54700
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 3.67 · 30 distinct chains · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, M	Flagellar basal-body rod protein FlgG	protein	260	23% helix, 33% strand	P0A1J3
L, U, V, W, X	Flagellar basal-body rod protein FlgG	protein	259	24% helix, 33% strand	P0A1J3
N	Flagellar basal-body rod protein FlgG	protein	251	24% helix, 32% strand	P0A1J3
O	Flagellar basal-body rod protein FlgG	protein	252	22% helix, 33% strand	P0A1J3
P	Flagellar basal-body rod protein FlgG	protein	248	23% helix, 31% strand	P0A1J3
Q, S	Flagellar basal-body rod protein FlgG	protein	247	25% helix, 33% strand	P0A1J3
R	Flagellar basal-body rod protein FlgG	protein	250	23% helix, 32% strand	P0A1J3
T	Flagellar basal-body rod protein FlgG	protein	253	25% helix, 31% strand	P0A1J3
a, c, d, e	Flagellar basal-body rod protein FlgF	protein	249	28% helix, 30% strand	P16323
b	Flagellar basal-body rod protein FlgF	protein	248	28% helix, 25% strand	P16323
0, 1, 2, 3, 4	Flagellar MS ring L2	protein	15	0% helix, 0% strand	—
5, 6, 7, 9, 8	Flagellar MS ring L1	protein	21	0% helix, 5% strand	P15928
f	Flagellar basal-body rod protein FlgC	protein	128	47% helix, 20% strand	P0A1I7
g	Flagellar basal-body rod protein FlgC	protein	130	49% helix, 18% strand	P0A1I7
h	Flagellar basal-body rod protein FlgC	protein	128	44% helix, 16% strand	P0A1I7
j	Flagellar basal-body rod protein FlgC	protein	127	48% helix, 17% strand	P0A1I7
l, m	Flagellar basal body rod protein FlgB	protein	106	64% helix, 5% strand	P16437
o	Flagellar basal body rod protein FlgB	protein	109	63% helix, 5% strand	P16437
p	Flagellar basal-body rod protein FlgC	protein	129	47% helix, 18% strand	P0A1I7
i	Flagellar basal-body rod protein FlgC	protein	129	44% helix, 16% strand	P0A1I7
k	Flagellar basal body rod protein FlgB	protein	108	62% helix, 5% strand	P16437
n	Flagellar basal body rod protein FlgB	protein	107	64% helix, 5% strand	P16437
q	Flagellar hook-basal body complex protein FliE	protein	71	80% helix, 0% strand	P26462
r	Flagellar hook-basal body complex protein FliE	protein	70	79% helix, 0% strand	P26462
s, t, u	Flagellar hook-basal body complex protein FliE	protein	72	82% helix, 0% strand	P26462
v	Flagellar hook-basal body complex protein FliE	protein	38	89% helix, 0% strand	P26462
DA, DB, DC, DD, DE, DF, DG, DH, DI, DJ, DK	Flagellar hook protein FlgE	protein	401	15% helix, 37% strand	P0A1J1
CE	Flagellar biosynthetic protein FliR	protein	260	70% helix, 0% strand	P54702
CA, CB, CC, CD	Flagellar biosynthetic protein FliQ	protein	89	80% helix, 0% strand	P0A1L5
w, x, y, z, CF	Flagellar biosynthetic protein FliP	protein	211	78% helix, 0% strand	P54700

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	1100	0.90	0.92	136	empty
2	870	0.90	0.92	115	empty
3	935	0.89	0.91	108	empty
4	1159	0.88	0.90	130	empty
5	1183	0.88	0.90	133	empty

Interfaces

315 interfaces between chains.

H–M · 2681 Å² buried · 25 hydrogen bonds · protein-protein
L–Q · 2666 Å² buried · 20 hydrogen bonds · protein-protein
I–N · 2645 Å² buried · 22 hydrogen bonds · protein-protein
J–O · 2631 Å² buried · 24 hydrogen bonds · protein-protein
K–P · 2591 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

P0A1J3 · AlphaFold monomer V2.0 prediction for flagellar basal-body rod protein flgg (P0A1J3) · a predicted model of the same protein · chain F against A, TM-score 0.97

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 P0A1J3
Every structure of UniProt P16323
Every structure of UniProt P15928
Every structure of UniProt P0A1I7
Every structure of UniProt P16437
Every structure of UniProt P26462
Every structure of UniProt P0A1J1
Every structure of UniProt P54702
Every structure of UniProt P0A1L5
Every structure of UniProt P54700
Elsewhere: RCSB PDB 7E80 · PDBe 7E80 · UniProt P0A1J3 · UniProt P16323 · UniProt P15928 · UniProt P0A1I7 · UniProt P16437 · UniProt P26462 · UniProt P0A1J1 · UniProt P54702 · UniProt P0A1L5 · UniProt P54700

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