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Crystal structure of the apsk domain of human PAPSS1 in complex with adpmg and paps

Analyse Crystal structure of the apsk domain of human PAPSS1 in complex with adpmg and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OFX
Type: protein
Length: 410 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1
EC: 2.7.1.25
UniProt: O43252
Ligands: PPS, ADP, MG, PO4
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (EC 2.7.1.25)	protein	205	42% helix, 14% strand	O43252

Ligands and binding sites

PPS · 3'-phosphate-adenosine-5'-phosphate sulfate · ligand · 2 copies · chains A, B
ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 4 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	190	0.73	0.90	36	MG, PPS, ADP
2	227	0.69	0.86	44	MG, PPS, ADP
3	94	0.46	0.80	21	empty
4	82	0.41	0.79	22	empty
5	61	0.26	0.73	14	empty

Interfaces

1 interface between chains.

A–B · 2756 Å² buried · 47 hydrogen bonds · protein-protein

Compared structures

2OFX · crystal structure of the APSK domain of human PAPSS1 in complex with ADPMg and PAPS · the same entry in another collection · chain A against A, TM-score 1.00
O43252 · AlphaFold monomer V2.0 prediction for bifunctional 3'-phosphoadenosine 5'-phosphosulfate… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 O43252
Elsewhere: RCSB PDB 2OFX · PDBe 2OFX · UniProt O43252

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