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8WKK: Cryo-EM structure of the whole rod with export apparatus and hook within the flagellar motor-hook complex in the CW state.

Analyse 8WKK: Cryo-EM structure of the whole rod with export apparatus and hook within… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8WKK
Type: protein
Length: 22,617 residues
Chains: 96
Method: electron microscopy
Authors: Tan, J.X., Zhang, L., Zhou, Y., Zhu, Y.Q.
Deposited: 09/28/23
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.3
Source: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Molecule: Flagellar biosynthetic protein FliQ; Flagellar biosynthetic protein FliR; Flagellar…
UniProt: P0A1L5, P54702, P54700, P26462, P16437, P0A1I7, P15928, P16323, P0A1J3, P0A1J1
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 3.3 · 31 distinct chains · 44% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Flagellar biosynthetic protein FliQ	protein	89	84% helix, 0% strand	P0A1L5
E	Flagellar biosynthetic protein FliR	protein	253	74% helix, 0% strand	P54702
F	Flagellar biosynthetic protein FliP	protein	207	79% helix, 0% strand	P54700
G	Flagellar biosynthetic protein FliP	protein	209	80% helix, 0% strand	P54700
H, I	Flagellar biosynthetic protein FliP	protein	208	77% helix, 0% strand	P54700
J	Flagellar biosynthetic protein FliP	protein	209	78% helix, 0% strand	P54700
K	Flagellar hook-basal body complex protein FliE	protein	40	83% helix, 0% strand	P26462
L	Flagellar hook-basal body complex protein FliE	protein	72	83% helix, 0% strand	P26462
M, N, O	Flagellar hook-basal body complex protein FliE	protein	74	80% helix, 0% strand	P26462
P	Flagellar hook-basal body complex protein FliE	protein	73	84% helix, 1% strand	P26462
Q	Flagellar basal body rod protein FlgB	protein	119	59% helix, 6% strand	P16437
R, S	Flagellar basal body rod protein FlgB	protein	108	66% helix, 5% strand	P16437
T	Flagellar basal body rod protein FlgB	protein	110	65% helix, 5% strand	P16437
U	Flagellar basal body rod protein FlgB	protein	106	69% helix, 5% strand	P16437
V, X, Y, Z, a	Flagellar basal-body rod protein FlgC	protein	133	44% helix, 20% strand	P0A1I7
W	Flagellar basal-body rod protein FlgC	protein	132	44% helix, 18% strand	P0A1I7
b	Flagellar M-ring protein	protein	13	0% helix, 15% strand	P15928
c, e, g, i, k	Flagellar M-ring protein	protein	16	19% helix, 6% strand	P15928
d, j	Flagellar M-ring protein	protein	20	0% helix, 10% strand	P15928
f, h, l	Flagellar M-ring protein	protein	21	0% helix, 14% strand	P15928
m	Flagellar basal-body rod protein FlgF	protein	248	28% helix, 31% strand	P16323
n, q	Flagellar basal-body rod protein FlgF	protein	249	27% helix, 30% strand	P16323
o, p	Flagellar basal-body rod protein FlgF	protein	250	29% helix, 31% strand	P16323
0, x, y, z	Flagellar basal-body rod protein FlgG	protein	248	24% helix, 32% strand	P0A1J3
1	Flagellar basal-body rod protein FlgG	protein	252	25% helix, 33% strand	P0A1J3
2, 3, 4, 5, 6, 7, 8, 9, ZA, ZB, ZC, ZD, ZE	Flagellar basal-body rod protein FlgG	protein	260	23% helix, 29% strand	P0A1J3
ZF, ZG, ZH, ZI, ZJ, ZK, ZL, ZM, ZN, ZO, ZP, ZQ, ZR, ZS, ZT, ZU, ZV, ZW, ZX, ZY, ZZ, Za, Zb, Zc, Zd, Ze, Zf, Zg, Zh	Flagellar hook protein FlgE	protein	401	15% helix, 40% strand	P0A1J1
r, u	Flagellar basal-body rod protein FlgG	protein	254	25% helix, 30% strand	P0A1J3
s, v	Flagellar basal-body rod protein FlgG	protein	255	25% helix, 30% strand	P0A1J3
t	Flagellar basal-body rod protein FlgG	protein	256	25% helix, 34% strand	P0A1J3
w	Flagellar basal-body rod protein FlgG	protein	243	24% helix, 31% strand	P0A1J3

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	1046	0.89	0.91	118	empty
2	1152	0.89	0.91	121	empty
3	1175	0.89	0.90	136	empty
4	907	0.89	0.91	104	empty
5	993	0.89	0.90	122	empty

Interfaces

384 interfaces between chains.

2–7 · 2737 Å² buried · 32 hydrogen bonds · protein-protein
1–w · 2701 Å² buried · 21 hydrogen bonds · protein-protein
0–5 · 2698 Å² buried · 27 hydrogen bonds · protein-protein
3–8 · 2692 Å² buried · 29 hydrogen bonds · protein-protein
2–x · 2682 Å² buried · 27 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 7 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 P0A1L5
Every structure of UniProt P54702
Every structure of UniProt P54700
Every structure of UniProt P26462
Every structure of UniProt P16437
Every structure of UniProt P0A1I7
Every structure of UniProt P15928
Every structure of UniProt P16323
Every structure of UniProt P0A1J3
Every structure of UniProt P0A1J1
Elsewhere: RCSB PDB 8WKK · PDBe 8WKK · UniProt P0A1L5 · UniProt P54702 · UniProt P54700 · UniProt P26462 · UniProt P16437 · UniProt P0A1I7 · UniProt P15928 · UniProt P16323 · UniProt P0A1J3 · UniProt P0A1J1

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