Research workbench

Three-dimensional model of SALMONELLA'S needle complex at subnanometer resolution

Analyse Three-dimensional model of SALMONELLA'S needle complex at subnanometer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Y9J
Type: protein
Length: 8,544 residues
Chains: 48
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein prgh; Lipoprotein prgk
UniProt: P41783, P41786
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 2 distinct chains · 40% helix, 25% 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	Protein prgh	protein	186	42% helix, 24% strand	P41783
Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v	Lipoprotein prgk	protein	170	37% helix, 26% strand	P41786

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	791	0.84	0.87	78	empty
2	895	0.84	0.85	102	empty
3	950	0.83	0.85	102	empty
4	705	0.83	0.87	79	empty
5	891	0.83	0.85	96	empty

Interfaces

96 interfaces between chains.

g–v · 2285 Å² buried · 60 hydrogen bonds · protein-protein
a–o · 2279 Å² buried · 57 hydrogen bonds · protein-protein
j–r · 2277 Å² buried · 57 hydrogen bonds · protein-protein
Z–u · 2276 Å² buried · 57 hydrogen bonds · protein-protein
f–k · 2274 Å² buried · 57 hydrogen bonds · protein-protein

Compared structures

P41783 · AlphaFold monomer V2.0 prediction for protein prgh (P41783) · a predicted model of the same protein · chain A against A, TM-score 0.98
P41786 · AlphaFold monomer V2.0 prediction for lipoprotein prgk (P41786) · a predicted model of the same protein · chain Y against A, TM-score 0.80

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 P41783
Every structure of UniProt P41786
Elsewhere: RCSB PDB 2Y9J · PDBe 2Y9J · UniProt P41783 · UniProt P41786

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