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Structure of para-ADP COMPLEX:TETRAGONAL form

Analyse Structure of para-ADP COMPLEX:TETRAGONAL form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EZ6
Type: protein
Length: 782 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plasmid partition protein a
UniProt: P07620
Ligands: ADP, MG
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Plasmid partition protein a	protein	388	52% helix, 12% strand	P07620
B	Plasmid partition protein a	protein	394	50% helix, 11% strand	P07620

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

7 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	1184	0.82	0.83	122	ADP, MG
2	176	0.48	0.76	26	empty
3	172	0.48	0.76	24	empty
4	65	0.45	0.82	18	empty
5	80	0.34	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 2764 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

3EZ6 · Structure of parA-ADP complex:tetragonal form · the same entry in another collection · chain A against A, TM-score 1.00
P07620 · AlphaFold monomer V2.0 prediction for plasmid partition protein a (P07620) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P07620
Elsewhere: RCSB PDB 3EZ6 · PDBe 3EZ6 · UniProt P07620

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