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Crystal structure of truncated flgd (monoclinic form) from the human pathogen helicobacter pylori (strain 26695)

Analyse Crystal structure of truncated flgd (monoclinic form) from the human pathogen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K5Y
Type: protein
Length: 584 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Basal-body rod modification protein flgd
UniProt: O25565
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Basal-body rod modification protein flgd	protein	146	4% helix, 49% strand	O25565

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	679	0.65	0.74	57	empty
2	518	0.60	0.74	42	empty
3	52	0.26	0.74	13	empty
4	53	0.24	0.72	11	empty

Interfaces

3 interfaces between chains.

A–B · 498 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 219 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 92 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5K5Y · Crystal structure of truncated FlgD (monoclinic form) from the human pathogen… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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Every structure of UniProt O25565
Elsewhere: RCSB PDB 5K5Y · PDBe 5K5Y · UniProt O25565

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