MolNFT v1 · #95999 · protein

Crystal structure of hfq from pseudomonas aeruginosa in complex with UTP

4J6X · Protein hfq: “Crystal structure of hfq from pseudomonas aeruginosa in complex with UTP”. X-ray diffraction, 1 ligand (UTP), 1 pocket (best druggability 0.71). MolNFT v1 #95999 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4J6X
Type: protein
Length: 401 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein hfq
UniProt: Q9HUM0
Ligands: UTP
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 19% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Protein hfq	protein	66	20% helix, 45% strand	Q9HUM0
B	Protein hfq	protein	67	19% helix, 43% strand	Q9HUM0
D	Protein hfq	protein	66	20% helix, 45% strand	Q9HUM0
E	Protein hfq	protein	68	19% helix, 46% strand	Q9HUM0
F	Protein hfq	protein	68	19% helix, 41% strand	Q9HUM0

Ligands and binding sites

UTP · Uridine 5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	916	0.71	0.76	60	empty

Interfaces

6 interfaces between chains.

E–F · 837 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 824 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 766 Å² buried · 11 hydrogen bonds · protein-protein
A–F · 765 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 740 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4J6X · Crystal structure of Hfq from Pseudomonas aeruginosa in complex with UTP · the same entry in another collection · chain F against F, TM-score 1.00
Q9HUM0 · AlphaFold monomer V2.0 prediction for RNA-binding protein hfq (Q9HUM0) · a predicted model of the same protein · chain E 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 Q9HUM0
Elsewhere: RCSB PDB 4J6X · PDBe 4J6X · UniProt Q9HUM0

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