MolNFT v1 · #27569 · protein

Aps complex of human paps synthetase 1

1XNJ · Bifunctional 3'-phosphoadenosine 5'-phosphosulfate…: “Aps complex of human paps synthetase 1”. X-ray diffraction, 2 ligands (ADX, ADP), 10 pockets (best druggability 0.75). MolNFT v1 #27569 on GenesisL1: 3D structure, binding sites…

PDB: 1XNJ
Type: protein
Length: 1,152 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1
EC: 2.7.7.4, 2.7.1.25
UniProt: O43252
Ligands: ADX, ADP
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (EC 2.7.7.4, 2.7.1.25)	protein	590	39% helix, 18% strand	O43252
A	Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (EC 2.7.7.4, 2.7.1.25)	protein	562	41% helix, 18% strand	O43252

Ligands and binding sites

ADX · Adenosine-5'-phosphosulfate · ligand · 3 copies · chains B, A
ADP · Adenosine-5'-diphosphate · ligand · chains B

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	493	0.75	0.83	49	ADX
2	689	0.75	0.80	66	empty
3	467	0.74	0.83	48	ADX
4	266	0.60	0.79	30	ADX
5	50	0.42	0.83	15	empty

Interfaces

1 interface between chains.

B–A · 3064 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

1XNJ · APS complex of human PAPS synthetase 1 · the same entry in another collection · chain B against B, TM-score 1.00
O43252 · AlphaFold monomer V2.0 prediction for bifunctional 3'-phosphoadenosine 5'-phosphosulfate… · a predicted model of the same protein · chain B 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 O43252
Elsewhere: RCSB PDB 1XNJ · PDBe 1XNJ · UniProt O43252

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