Research workbench
Crystal structrue of deletion mutant of aps-kinase domain of human paps-synthetase 1 in complex with cyclic paps and dadp
Analyse Crystal structrue of deletion mutant of aps-kinase domain of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PEZ
- Type
- protein
- Length
- 335 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (paps synthetase 1)…
- UniProt
- O43252
- Ligands
- DAT, GGZ
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (paps synthetase 1) (papss 1) (sulfurylase kinase 1) (SK1) (sk 1) | protein | 176 | 44% helix, 16% strand | O43252 |
| B | Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (paps synthetase 1) (papss 1) (sulfurylase kinase 1) (SK1) (sk 1) | protein | 159 | 45% helix, 17% strand | O43252 |
Ligands and binding sites
- DAT · 2'-deoxyadenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- GGZ · (2s,3ar,4r,6r,6ar)-4-(6-amino-9H-purin-9-yl)-6-({[(R)-hydroxy(sulfooxy)phosphoryl]oxy}methyl)tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-2-ol 2-oxide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.60 | 0.77 | 42 | GGZ, DAT |
| 2 | 185 | 0.48 | 0.76 | 32 | DAT |
Interfaces
1 interface between chains.
- A–B · 796 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2PEZ · Crystal structrue of deletion mutant of APS-kinase domain of human PAPS-synthetase 1 in… · 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 0.99
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 2PEZ · PDBe 2PEZ · UniProt O43252
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