MolNFT v1 · #46817 · protein

Crystal structure of the apsk domain of human PAPSS1 complexed with 2 aps molecules

2OFW · Aps kinase domain of the paps synthetase 1: “Crystal structure of the apsk domain of human PAPSS1 complexed with 2 aps molecules”. X-ray diffraction, 2 ligands (ADX, MG), 15 pockets (best druggability 0.87). MolNFT v1 #46817 on…

PDB: 2OFW
Type: protein
Length: 1,602 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aps kinase domain of the paps synthetase 1
EC: 2.7.1.25
UniProt: O43252
Ligands: ADX, MG
Pockets: 15 · best druggability 0.87

Structure

x-ray diffraction · 5 distinct chains · 42% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aps kinase domain of the paps synthetase 1 (EC 2.7.1.25)	protein	200	43% helix, 14% strand	O43252
B, H	Aps kinase domain of the paps synthetase 1 (EC 2.7.1.25)	protein	193	42% helix, 14% strand	O43252
C, D, F	Aps kinase domain of the paps synthetase 1 (EC 2.7.1.25)	protein	204	43% helix, 14% strand	O43252
E	Aps kinase domain of the paps synthetase 1 (EC 2.7.1.25)	protein	203	42% helix, 14% strand	O43252
G	Aps kinase domain of the paps synthetase 1 (EC 2.7.1.25)	protein	201	41% helix, 14% strand	O43252

Ligands and binding sites

ADX · Adenosine-5'-phosphosulfate · ligand · 16 copies · chains A, B, C, D, E, F, G, H
MG · Magnesium ion · metal · 6 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

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	912	0.87	0.89	126	MG, ADX
2	652	0.84	0.88	94	MG, ADX
3	1007	0.79	0.81	93	MG, ADX
4	257	0.77	0.90	43	MG, ADX
5	289	0.72	0.85	39	MG, ADX

Interfaces

13 interfaces between chains.

C–D · 2668 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 2563 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 1879 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 1878 Å² buried · 22 hydrogen bonds · protein-protein
C–F · 359 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2OFW · Crystal structure of the APSK domain of human PAPSS1 complexed with 2 APS molecules · the same entry in another collection · chain H against H, 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 0.98

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 2OFW · PDBe 2OFW · UniProt O43252

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.