Research workbench

8WL2: Cryo-EM structure of the membrane-anchored part of the flagellar motor-hook complex in the CW state.

Analyse 8WL2: Cryo-EM structure of the membrane-anchored part of the flagellar… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8WL2
Type: protein
Length: 45,378 residues
Chains: 213
Method: electron microscopy
Authors: Tan, J.X., Zhang, L., Zhou, Y., Zhu, Y.Q.
Deposited: 09/29/23
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.4
Source: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Molecule: Flagellar L-ring protein; Flagellar P-ring protein; Flagellar basal-body rod protein…
UniProt: P0A1N8, P15930, P0A1J3, P0A1J1, P16323, P15928, P0A1L5, P54702, P54700, P26462, P16437, P0A1I7
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 3.4 · 51 distinct chains · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	Flagellar L-ring protein	protein	211	14% helix, 45% strand	P0A1N8
a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z	Flagellar P-ring protein	protein	303	22% helix, 32% strand	P15930
0, AL, AM, AN	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
AA	Flagellar basal-body rod protein FlgF	protein	248	28% helix, 31% strand	P16323
AB, AE	Flagellar basal-body rod protein FlgF	protein	249	27% helix, 30% strand	P16323
AC, AD	Flagellar basal-body rod protein FlgF	protein	250	29% helix, 31% strand	P16323
AF, AI	Flagellar basal-body rod protein FlgG	protein	254	25% helix, 30% strand	P0A1J3
AG, AJ	Flagellar basal-body rod protein FlgG	protein	255	25% helix, 30% strand	P0A1J3
AH	Flagellar basal-body rod protein FlgG	protein	256	25% helix, 34% strand	P0A1J3
AK	Flagellar basal-body rod protein FlgG	protein	243	24% helix, 31% strand	P0A1J3
AR, AS, AT, AU, AV, AW, AX, AY, AZ, Aa, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, AO, AP, AQ, BR, BS, BT, BU, BV, BW, BX	Flagellar M-ring protein	protein	164	26% helix, 43% strand	P15928
Ab, Aq, Ar, As	Flagellar biosynthetic protein FliQ	protein	89	84% helix, 0% strand	P0A1L5
At	Flagellar biosynthetic protein FliR	protein	253	74% helix, 0% strand	P54702
Au	Flagellar biosynthetic protein FliP	protein	207	79% helix, 0% strand	P54700
Av	Flagellar biosynthetic protein FliP	protein	209	80% helix, 0% strand	P54700
Aw, Ax	Flagellar biosynthetic protein FliP	protein	208	77% helix, 1% strand	P54700
Ay	Flagellar biosynthetic protein FliP	protein	209	78% helix, 0% strand	P54700
Az	Flagellar hook-basal body complex protein FliE	protein	59	85% helix, 0% strand	P26462
A1	Flagellar hook-basal body complex protein FliE	protein	91	85% helix, 0% strand	P26462
A2, A3, A4	Flagellar hook-basal body complex protein FliE	protein	93	82% helix, 0% strand	P26462
A5	Flagellar hook-basal body complex protein FliE	protein	92	85% helix, 1% strand	P26462
A6	Flagellar basal body rod protein FlgB	protein	134	52% helix, 7% strand	P16437
A7	Flagellar basal body rod protein FlgB	protein	121	59% helix, 4% strand	P16437
A8	Flagellar basal body rod protein FlgB	protein	125	56% helix, 4% strand	P16437
A9	Flagellar basal body rod protein FlgB	protein	127	57% helix, 4% strand	P16437
A0	Flagellar basal body rod protein FlgB	protein	123	59% helix, 4% strand	P16437
UI, UJ, UK, UL, UM, UN, UO, UP	Flagellar M-ring protein	protein	155	40% helix, 21% strand	P15928
BA, BC, BD, BE, BF	Flagellar basal-body rod protein FlgC	protein	133	44% helix, 20% strand	P0A1I7
BB	Flagellar basal-body rod protein FlgC	protein	132	44% helix, 18% strand	P0A1I7
WA	Flagellar M-ring protein	protein	113	35% helix, 20% strand	P15928
WB	Flagellar M-ring protein	protein	111	38% helix, 20% strand	P15928
WC	Flagellar M-ring protein	protein	108	35% helix, 20% strand	P15928
WD	Flagellar M-ring protein	protein	110	39% helix, 20% strand	P15928
WE, WG, WU	Flagellar M-ring protein	protein	112	37% helix, 20% strand	P15928
WF, WQ, WR, WS, WT, WW	Flagellar M-ring protein	protein	111	37% helix, 20% strand	P15928
WH, WI	Flagellar M-ring protein	protein	95	37% helix, 23% strand	P15928
WJ	Flagellar M-ring protein	protein	99	38% helix, 22% strand	P15928
WK	Flagellar M-ring protein	protein	98	39% helix, 22% strand	P15928
WL	Flagellar M-ring protein	protein	85	42% helix, 26% strand	P15928
WM	Flagellar M-ring protein	protein	82	40% helix, 27% strand	P15928
WN	Flagellar M-ring protein	protein	84	40% helix, 26% strand	P15928
WO	Flagellar M-ring protein	protein	96	36% helix, 24% strand	P15928
WP	Flagellar M-ring protein	protein	100	37% helix, 22% strand	P15928
WV	Flagellar M-ring protein	protein	110	37% helix, 20% strand	P15928
BG	Flagellar M-ring protein	protein	13	0% helix, 15% strand	P15928
BH, BJ, BL, BN, BP	Flagellar M-ring protein	protein	16	19% helix, 6% strand	P15928
BI, BO	Flagellar M-ring protein	protein	20	0% helix, 10% strand	P15928
BK, BM, BQ	Flagellar M-ring protein	protein	21	0% helix, 14% strand	P15928

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	1230	0.90	0.92	156	empty
2	963	0.90	0.92	142	empty
3	963	0.90	0.92	130	empty
4	1309	0.89	0.91	123	empty
5	1193	0.89	0.91	123	empty

Interfaces

1,022 interfaces between chains.

o–p · 3604 Å² buried · 52 hydrogen bonds · protein-protein
y–z · 3599 Å² buried · 52 hydrogen bonds · protein-protein
m–n · 3598 Å² buried · 52 hydrogen bonds · protein-protein
s–t · 3597 Å² buried · 52 hydrogen bonds · protein-protein
f–g · 3597 Å² buried · 52 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 26 disulfide (disulfide).

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 P0A1N8
Every structure of UniProt P15930
Every structure of UniProt P0A1J3
Every structure of UniProt P0A1J1
Every structure of UniProt P16323
Every structure of UniProt P15928
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
Elsewhere: RCSB PDB 8WL2 · PDBe 8WL2 · UniProt P0A1N8 · UniProt P15930 · UniProt P0A1J3 · UniProt P0A1J1 · UniProt P16323 · UniProt P15928 · UniProt P0A1L5 · UniProt P54702 · UniProt P54700 · UniProt P26462 · UniProt P16437 · UniProt P0A1I7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.