Research workbench

Hipb-O1-O2 COMPLEX/P21212 crystal form

Analyse Hipb-O1-O2 COMPLEX/P21212 crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YG1
Type: protein + DNA
Length: 377 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antitoxin hipb; DNA (48-mer)
UniProt: P23873
Pockets: 11 · best druggability 0.58

Structure

x-ray diffraction · 5 distinct chains · 58% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antitoxin hipb	protein	72	60% helix, 10% strand	P23873
B, C	Antitoxin hipb	protein	69	58% helix, 10% strand	P23873
D	Antitoxin hipb	protein	71	58% helix, 6% strand	P23873
F	DNA (48-mer)	dna	48	—	—
T	DNA (48-mer)	dna	48	—	—

Pockets

11 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	234	0.58	0.80	28	empty
2	233	0.57	0.80	26	empty
3	171	0.53	0.79	19	empty
4	143	0.51	0.80	18	empty
5	142	0.49	0.79	13	empty

Interfaces

11 interfaces between chains.

F–T · 2081 Å² buried · 153 hydrogen bonds · nucleic-nucleic
A–B · 1439 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1407 Å² buried · 26 hydrogen bonds · protein-protein
D–T · 386 Å² buried · 8 hydrogen bonds · protein-nucleic
B–F · 378 Å² buried · 5 hydrogen bonds · protein-nucleic

Compared structures

4YG1 · HipB-O1-O2 complex/P21212 crystal form · the same entry in another collection · chain T against T, TM-score 1.00
P23873 · AlphaFold monomer V2.0 prediction for antitoxin hipb (P23873) · a predicted model of the same protein · chain B 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 4YG1 · PDBe 4YG1 · UniProt P23873

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