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Crystal structures of holliday junction resolvases from archaeoglobus fulgidus bound to DNA substrate

Analyse Crystal structures of holliday junction resolvases from archaeoglobus fulgidus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WJ0
Type: protein + DNA
Length: 298 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Archaeal hjc; Half-junction
UniProt: O28314
Ligands: NCO
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Archaeal hjc	protein	125	31% helix, 31% strand	O28314
B	Archaeal hjc	protein	125	29% helix, 30% strand	O28314
C	Half-junction	dna	24	—	—
D	Half-junction	dna	24	—	—

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · chains B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	785	0.72	0.78	56	empty
2	83	0.46	0.81	24	NCO
3	81	0.33	0.74	11	empty

Interfaces

5 interfaces between chains.

A–B · 860 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 557 Å² buried · 42 hydrogen bonds · nucleic-nucleic
B–C · 371 Å² buried · 8 hydrogen bonds · protein-nucleic
A–D · 183 Å² buried · 4 hydrogen bonds · protein-nucleic
B–D · 70 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

2WJ0 · Crystal structures of Holliday junction resolvases from Archaeoglobus fulgidus bound to… · the same entry in another collection · chain A against A, TM-score 1.00
O28314 · AlphaFold monomer V2.0 prediction for holliday junction resolvase hjc (O28314) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O28314
Elsewhere: RCSB PDB 2WJ0 · PDBe 2WJ0 · UniProt O28314

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