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Crystal structure of shaft pilin spad from lactobacillus rhamnosus gg

Analyse Crystal structure of shaft pilin spad from lactobacillus rhamnosus gg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YU5
Type: protein
Length: 892 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pilus assembly protein
UniProt: A0A179XFF5
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pilus assembly protein	protein	444	9% helix, 45% strand	A0A179XFF5
B	Pilus assembly protein	protein	448	9% helix, 45% strand	A0A179XFF5

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	543	0.68	0.78	56	empty
2	486	0.62	0.75	52	empty
3	56	0.31	0.76	18	empty
4	51	0.25	0.73	13	empty

Interfaces

1 interface between chains.

A–B · 898 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 isopeptide (isopeptide).

Compared structures

5YU5 · Crystal structure of shaft pilin spaD from Lactobacillus rhamnosus GG · 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 A0A179XFF5
Elsewhere: RCSB PDB 5YU5 · PDBe 5YU5 · UniProt A0A179XFF5

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