Research workbench

Structure of hipa-hipb-O2-O3 complex

Analyse Structure of hipa-hipb-O2-O3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K98
Type: protein + DNA
Length: 1,016 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase hipa; Antitoxin hipb; DNA (5'…
EC: 2.7.11.1
UniProt: P23874, M9IJX7
Pockets: 15 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	SERINE/THREONINE-protein kinase hipa (EC 2.7.11.1)	protein	414	36% helix, 21% strand	P23874
B, P	Antitoxin hipb	protein	71	56% helix, 13% strand	M9IJX7
T	DNA (5'- D(TPCPCPCPTPAPTPCPCPCPCPTPTPAPAPGPGPGPGPAPTPAP* G)-3')	dna	23	—	—
E	DNA (5'- D(CPTPAPTPCPCPCPCPTPTPAPAPGPGPGPGPAPTPAPGPGPGP* a)-3')	dna	23	—	—

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	130	0.79	0.97	32	empty
2	129	0.79	0.97	31	empty
3	1064	0.74	0.77	89	empty
4	667	0.70	0.78	80	empty
5	90	0.68	0.92	19	empty

Interfaces

13 interfaces between chains.

B–P · 1425 Å² buried · 20 hydrogen bonds · protein-protein
T–E · 1130 Å² buried · 54 hydrogen bonds · nucleic-nucleic
D–P · 542 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 538 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 405 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

5K98 · Structure of HipA-HipB-O2-O3 complex · the same entry in another collection · chain T against T, TM-score 1.00
P23874 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase toxin hipa (P23874) · a predicted model of the same protein · chain A 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 P23874
Every structure of UniProt M9IJX7
Elsewhere: RCSB PDB 5K98 · PDBe 5K98 · UniProt P23874 · UniProt M9IJX7

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