Research workbench

Deinococcus radiodurans ISDRA2 transposase right end DNA complex

Analyse Deinococcus radiodurans ISDRA2 transposase right end DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XMA
Type: protein + DNA
Length: 689 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transposase; DRA2 transposase right end recognition site
UniProt: O83028
Ligands: MG
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 39% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Transposase	protein	139	39% helix, 37% strand	O83028
B	Transposase	protein	135	40% helix, 36% strand	O83028
C, D, G	DRA2 transposase right end recognition site	dna	34	—	—
E	Transposase	protein	141	37% helix, 35% strand	O83028
H	DRA2 transposase right end recognition site	dna	33	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H

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

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	616	0.81	0.86	72	empty
2	588	0.80	0.86	87	empty
3	227	0.60	0.81	24	MG
4	203	0.59	0.82	22	MG
5	229	0.59	0.81	26	MG

Interfaces

17 interfaces between chains.

A–B · 1900 Å² buried · 36 hydrogen bonds · protein-protein
E–F · 1894 Å² buried · 37 hydrogen bonds · protein-protein
E–G · 1248 Å² buried · 33 hydrogen bonds · protein-nucleic
A–C · 1241 Å² buried · 31 hydrogen bonds · protein-nucleic
F–H · 1236 Å² buried · 30 hydrogen bonds · protein-nucleic

Compared structures

2XMA · Deinococcus radiodurans ISDRA2 transposase right end DNA complex · the same entry in another collection · chain A against A, TM-score 1.00

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 O83028
Elsewhere: RCSB PDB 2XMA · PDBe 2XMA · UniProt O83028

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