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Crystal structure of hfq in complex with the srna rydc

Analyse Crystal structure of hfq in complex with the srna rydc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4V2S
Type: protein + RNA
Length: 474 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding protein hfq; Rydc
UniProt: P0A6X3
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 18% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-binding protein hfq	protein	71	18% helix, 44% strand	P0A6X3
B	RNA-binding protein hfq	protein	70	19% helix, 44% strand	P0A6X3
C	RNA-binding protein hfq	protein	68	19% helix, 46% strand	P0A6X3
D	RNA-binding protein hfq	protein	71	15% helix, 44% strand	P0A6X3
E	RNA-binding protein hfq	protein	67	16% helix, 46% strand	P0A6X3
F	RNA-binding protein hfq	protein	70	17% helix, 44% strand	P0A6X3
Q	Rydc	rna	57	—	—

Pockets

7 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	905	0.79	0.82	54	empty
2	324	0.54	0.76	19	empty
3	95	0.38	0.76	19	empty
4	100	0.38	0.75	18	empty
5	100	0.31	0.72	15	empty

Interfaces

12 interfaces between chains.

D–E · 834 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 763 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 757 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 726 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 722 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4V2S · Crystal structure of Hfq in complex with the sRNA RydC · the same entry in another collection · chain Q against Q, TM-score 1.00
P0A6X3 · AlphaFold monomer V2.0 prediction for RNA-binding protein hfq (P0A6X3) · a predicted model of the same protein · chain E against A, TM-score 0.96

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 4V2S · PDBe 4V2S · UniProt P0A6X3

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