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Crystal structure of the outer membrane complex of a type IV secretion system

Analyse Crystal structure of the outer membrane complex of a type IV secretion system in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3JQO
Type: protein
Length: 4,909 residues
Chains: 42
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Traf protein; Trao protein; Tran protein
UniProt: Q46705, Q46704, Q46702
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 14 distinct chains · 17% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, Y	Traf protein	protein	195	20% helix, 37% strand	Q46705
B, E, H, K, N, Q, T, W, Z, c, f, i, l, o	Trao protein	protein	130	13% helix, 35% strand	Q46704
C	Tran protein	protein	26	0% helix, 12% strand	Q46702
F, I, g, j, m	Tran protein	protein	25	0% helix, 12% strand	Q46702
G	Traf protein	protein	193	20% helix, 37% strand	Q46705
J, M, P, S	Traf protein	protein	197	20% helix, 37% strand	Q46705
L	Tran protein	protein	28	0% helix, 11% strand	Q46702
O, X, a, d	Tran protein	protein	24	0% helix, 13% strand	Q46702
R	Tran protein	protein	24	0% helix, 13% strand	Q46702
U	Tran protein	protein	27	0% helix, 11% strand	Q46702
V, e, k	Traf protein	protein	196	21% helix, 37% strand	Q46705
b, h	Traf protein	protein	195	18% helix, 37% strand	Q46705
n	Traf protein	protein	196	19% helix, 37% strand	Q46705
p	Tran protein	protein	23	0% helix, 13% strand	Q46702

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains D, E, H, h, i, l, k, o
LDA · Lauryl dimethylamine-N-oxide · additive · chains A, D, J

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	73	0.74	0.98	25	empty
2	66	0.73	0.98	25	empty
3	64	0.72	0.98	24	empty
4	66	0.72	0.97	26	empty
5	57	0.72	0.99	25	empty

Interfaces

128 interfaces between chains.

k–n · 2413 Å² buried · 36 hydrogen bonds · protein-protein
M–P · 2406 Å² buried · 36 hydrogen bonds · protein-protein
P–S · 2401 Å² buried · 32 hydrogen bonds · protein-protein
b–e · 2400 Å² buried · 34 hydrogen bonds · protein-protein
S–V · 2379 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 112 modified, 14 disulfide (engineered, disulfide).

Compared structures

3JQO · Crystal structure of the outer membrane complex of a type IV secretion system · the same entry in another collection · chain B against B, 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 Q46705
Every structure of UniProt Q46704
Every structure of UniProt Q46702
Elsewhere: RCSB PDB 3JQO · PDBe 3JQO · UniProt Q46705 · UniProt Q46704 · UniProt Q46702

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