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Structure of diol dehydratase-reactivating factor complexed with ADP and MG2+

Analyse Structure of diol dehydratase-reactivating factor complexed with ADP and MG2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2D0O
Type: protein
Length: 1,426 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diol dehydratase-reactivating factor large subunit; Diol dehydratase-reactivating factor…
Ligands: ADP, MG, SO4
Pockets: 16 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Diol dehydratase-reactivating factor large subunit	protein	606	33% helix, 31% strand	—
B	Diol dehydratase-reactivating factor small subunit	protein	108	35% helix, 25% strand	—
C	Diol dehydratase-reactivating factor large subunit	protein	604	33% helix, 32% strand	—
D	Diol dehydratase-reactivating factor small subunit	protein	108	37% helix, 25% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 2 copies · chains A, C

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

Pockets

16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	824	0.86	0.88	83	empty
2	205	0.74	0.90	41	MG, ADP
3	212	0.73	0.89	40	MG, ADP
4	322	0.73	0.85	55	empty
5	304	0.68	0.83	58	empty

Interfaces

6 interfaces between chains.

A–C · 1988 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 874 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 779 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 311 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 307 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2D0O · Structure of diol dehydratase-reactivating factor complexed with ADP and Mg2+ · 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
Elsewhere: RCSB PDB 2D0O · PDBe 2D0O

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