MolNFT v1 · #55469 · protein

Structure of salmonella typhimurium hfq at 1.15 a

2YLB · Protein hfq: “Structure of salmonella typhimurium hfq at 1.15 a”. X-ray diffraction, 3 pockets (best druggability 0.63). MolNFT v1 #55469 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YLB
Type: protein
Length: 400 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein hfq
UniProt: P0A1R0
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 4 distinct chains · 21% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein hfq	protein	65	22% helix, 46% strand	P0A1R0
B	Protein hfq	protein	65	20% helix, 46% strand	P0A1R0
C, D, E	Protein hfq	protein	68	21% helix, 44% strand	P0A1R0
F	Protein hfq	protein	66	21% helix, 45% strand	P0A1R0

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	426	0.63	0.77	22	empty
2	170	0.43	0.73	29	empty
3	102	0.33	0.72	20	empty

Interfaces

6 interfaces between chains.

A–B · 814 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 797 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 783 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 773 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 766 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

2YLB · Structure of Salmonella typhimurium Hfq at 1.15 A · the same entry in another collection · chain F against F, TM-score 1.00
P0A1R0 · AlphaFold monomer V2.0 prediction for RNA-binding protein hfq (P0A1R0) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P0A1R0
Elsewhere: RCSB PDB 2YLB · PDBe 2YLB · UniProt P0A1R0

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