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A cooperative pnpase-hfq-RNA carrier complex facilitates bacterial riboregulation. pnpase-3'ETS(LEUZ)-hfq

Analyse A cooperative pnpase-hfq-RNA carrier complex facilitates bacterial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OGM
Type: protein + RNA
Length: 2,503 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding protein hfq; Polyribonucleotide nucleotidyltransferase; 3'ETS(LEUZ)
EC: 2.7.7.8
UniProt: A1AJ78, P05055
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 8 distinct chains · 31% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
K	RNA-binding protein hfq	protein	62	21% helix, 44% strand	A1AJ78
J, I	RNA-binding protein hfq	protein	63	21% helix, 46% strand	A1AJ78
D	RNA-binding protein hfq	protein	67	18% helix, 42% strand	A1AJ78
E, F	RNA-binding protein hfq	protein	61	21% helix, 49% strand	A1AJ78
L	Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8)	protein	693	31% helix, 26% strand	P05055
N	Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8)	protein	689	33% helix, 25% strand	P05055
O	Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8)	protein	695	32% helix, 23% strand	P05055
P	3'ETS(LEUZ)	rna	49	—	—

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1061	0.82	0.83	100	empty
2	1072	0.81	0.82	109	empty
3	584	0.78	0.85	80	empty
4	296	0.71	0.85	41	empty
5	234	0.71	0.86	40	empty

Interfaces

20 interfaces between chains.

N–O · 1754 Å² buried · 25 hydrogen bonds · protein-protein
L–O · 1719 Å² buried · 20 hydrogen bonds · protein-protein
L–N · 1716 Å² buried · 20 hydrogen bonds · protein-protein
L–P · 706 Å² buried · 9 hydrogen bonds · protein-nucleic
J–P · 619 Å² buried · 16 hydrogen bonds · protein-nucleic

Compared structures

7OGM · A cooperative PNPase-Hfq-RNA carrier complex facilitates bacterial riboregulation.… · the same entry in another collection · chain P against P, TM-score 1.00
P05055 · AlphaFold monomer V2.0 prediction for polyribonucleotide nucleotidyltransferase (P05055) · a predicted model of the same protein · chain N against A, TM-score 0.92
A1AJ78 · AlphaFold monomer V2.0 prediction for RNA-binding protein hfq (A1AJ78) · a predicted model of the same protein · chain K against A, TM-score 0.91

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 A1AJ78
Every structure of UniProt P05055
Elsewhere: RCSB PDB 7OGM · PDBe 7OGM · UniProt A1AJ78 · UniProt P05055

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