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N-terminal domain of Helicobacter pylori LlaJI.R1

Analyse N-terminal domain of Helicobacter pylori LlaJI.R1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6C5D
Type: protein
Length: 504 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.97
Source: Helicobacter pylori
Molecule: LlaJI.R1
UniProt: Q9ZMQ4
Pockets: 6 · best druggability 0.42

Structure

x-ray diffraction · resolution 1.97 · 2 distinct chains · 27% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	LlaJI.R1	protein	121	29% helix, 32% strand	Q9ZMQ4
D, B	LlaJI.R1	protein	131	25% helix, 35% strand	Q9ZMQ4

Pockets

6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.42	0.77	18	empty
2	96	0.39	0.76	17	empty
3	65	0.36	0.78	11	empty
4	69	0.34	0.76	16	empty
5	52	0.32	0.77	12	empty

Interfaces

3 interfaces between chains.

D–C · 898 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 853 Å² buried · 6 hydrogen bonds · protein-protein
D–B · 41 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

6C5D · N-terminal domain of helicobacter pylori LLAJI.R1 · 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
Every structure of UniProt Q9ZMQ4
Elsewhere: RCSB PDB 6C5D · PDBe 6C5D · UniProt Q9ZMQ4

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