Research workbench

Polyala model of the prc from the type 4 secretion system of H. pylori

Analyse Polyala model of the prc from the type 4 secretion system of H. pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ODJ
Type: protein
Length: 5,083 residues
Chains: 17
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyala model of prc from H.PYLORI
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 30% helix, 13% 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	Polyala model of prc from H.PYLORI	protein	299	30% helix, 13% strand	—

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	930	0.84	0.85	142	empty
2	872	0.83	0.85	134	empty
3	882	0.83	0.85	127	empty
4	1129	0.81	0.83	141	empty
5	1033	0.81	0.83	123	empty

Interfaces

34 interfaces between chains.

G–H · 1574 Å² buried · 2 hydrogen bonds · protein-protein
I–P · 1573 Å² buried · 3 hydrogen bonds · protein-protein
M–N · 1568 Å² buried · 2 hydrogen bonds · protein-protein
L–M · 1567 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 1561 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6ODJ · PolyAla Model of the PRC from the Type 4 Secretion System of H. pylori · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 6ODJ · PDBe 6ODJ

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