Research workbench
Crystal structure of human phosphoribosylpyrophosphate synthetase- associated protein 39 (PAP39)
Analyse Crystal structure of human phosphoribosylpyrophosphate synthetase- associated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C4K
- Type
- protein
- Length
- 1,830 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosyl pyrophosphate synthetase-associated protein 1
- UniProt
- Q14558
- Ligands
- TAM, SO4
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Phosphoribosyl pyrophosphate synthetase-associated protein 1 | protein | 305 | 37% helix, 24% strand | Q14558 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, E, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.77 | 0.80 | 101 | SO4 |
| 2 | 656 | 0.69 | 0.77 | 76 | SO4 |
| 3 | 609 | 0.69 | 0.78 | 63 | SO4 |
| 4 | 649 | 0.69 | 0.77 | 66 | SO4 |
| 5 | 356 | 0.62 | 0.78 | 50 | empty |
Interfaces
6 interfaces between chains.
- B–E · 2168 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 1199 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 1183 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 301 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 255 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2C4K · Crystal structure of human phosphoribosylpyrophosphate synthetase- associated protein 39… · the same entry in another collection · chain C against C, TM-score 1.00
- Q14558 · AlphaFold monomer V2.0 prediction for phosphoribosyl pyrophosphate synthase-associated… · 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 Q14558
- Elsewhere: RCSB PDB 2C4K · PDBe 2C4K · UniProt Q14558
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