Research workbench
Crystal structure of human atic in complex with xmp
Analyse Crystal structure of human atic in complex with xmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PKX
- Type
- protein
- Length
- 2,353 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional purine biosynthesis protein purh
- EC
- 2.1.2.3, 3.5.4.10
- UniProt
- P31939
- Ligands
- XMP, K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional purine biosynthesis protein purh (EC 2.1.2.3, 3.5.4.10) | protein | 588 | 43% helix, 19% strand | P31939 |
| B, D | Bifunctional purine biosynthesis protein purh (EC 2.1.2.3, 3.5.4.10) | protein | 589 | 44% helix, 19% strand | P31939 |
| C | Bifunctional purine biosynthesis protein purh (EC 2.1.2.3, 3.5.4.10) | protein | 587 | 44% helix, 19% strand | P31939 |
Ligands and binding sites
- XMP · Xanthosine-5'-monophosphate · ligand · 2 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.85 | 0.97 | 45 | empty |
| 2 | 256 | 0.84 | 0.96 | 47 | empty |
| 3 | 1163 | 0.80 | 0.81 | 131 | empty |
| 4 | 645 | 0.76 | 0.81 | 71 | empty |
| 5 | 971 | 0.75 | 0.78 | 98 | empty |
Interfaces
4 interfaces between chains.
- A–B · 6134 Ų buried · 79 hydrogen bonds · protein-protein
- C–D · 6050 Ų buried · 81 hydrogen bonds · protein-protein
- A–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1PKX · Crystal Structure of human ATIC in complex with XMP · the same entry in another collection · chain A against A, TM-score 1.00
- P31939 · AlphaFold monomer V2.0 prediction for bifunctional purine biosynthesis protein atic… · a predicted model of the same protein · chain C 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 P31939
- Elsewhere: RCSB PDB 1PKX · PDBe 1PKX · UniProt P31939
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