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Crystal structure of the complex of the E. COLI hfq with POLY(A)

Analyse Crystal structure of the complex of the E. COLI hfq with POLY(A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GIB
Type: protein + RNA
Length: 200 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein hfq; 5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'
UniProt: P0A6X3
Pockets: 1 · best druggability 0.29

Structure

x-ray diffraction · 4 distinct chains · 20% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein hfq	protein	64	20% helix, 48% strand	P0A6X3
B	Protein hfq	protein	65	20% helix, 46% strand	P0A6X3
C	Protein hfq	protein	62	21% helix, 50% strand	P0A6X3
H	5'-R(PAPAPAPAPAPAPAPAP*A)-3'	rna	9	—	—

Ligands and binding sites

NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	58	0.29	0.74	12	NHE

Interfaces

5 interfaces between chains.

B–C · 763 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 698 Å² buried · 10 hydrogen bonds · protein-protein
B–H · 441 Å² buried · 8 hydrogen bonds · protein-nucleic
C–H · 438 Å² buried · 10 hydrogen bonds · protein-nucleic
A–H · 366 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

3GIB · Crystal Structure of the Complex of the E. coli Hfq with Poly(A) · the same entry in another collection · chain A against A, TM-score 1.00
P0A6X3 · AlphaFold monomer V2.0 prediction for RNA-binding protein hfq (P0A6X3) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P0A6X3
Elsewhere: RCSB PDB 3GIB · PDBe 3GIB · UniProt P0A6X3

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