Research workbench

Hipb-O1-O1* complex

Analyse Hipb-O1-O1* complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YG4
Type: protein + DNA
Length: 326 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antitoxin hipb; DNA (28-mer); DNA (5'- D(*AP*TP*AP*TP*CP*CP*CP*CP*TP*TP*AP*AP*GP*GP*GP*GP*…
UniProt: P23873
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 4 distinct chains · 59% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Antitoxin hipb	protein	69	59% helix, 13% strand	P23873
B	Antitoxin hipb	protein	71	58% helix, 11% strand	P23873
T	DNA (28-mer)	dna	28	—	—
F	DNA (5'- D(APTPAPTPCPCPCPCPTPTPAPAPGPGPGPGPAPTPAPA)-3')	dna	20	—	—

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	412	0.61	0.77	29	empty
2	238	0.58	0.80	20	empty
3	236	0.56	0.79	27	empty
4	180	0.50	0.78	19	empty

Interfaces

10 interfaces between chains.

C–D · 1388 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1358 Å² buried · 23 hydrogen bonds · protein-protein
T–F · 878 Å² buried · 76 hydrogen bonds · nucleic-nucleic
B–F · 396 Å² buried · 12 hydrogen bonds · protein-nucleic
A–T · 370 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

4YG4 · HipB-O1-O1* complex · the same entry in another collection · chain D against D, TM-score 1.00
P23873 · AlphaFold monomer V2.0 prediction for antitoxin hipb (P23873) · a predicted model of the same protein · chain A 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 P23873
Elsewhere: RCSB PDB 4YG4 · PDBe 4YG4 · UniProt P23873

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