Research workbench
Crystal structure of aicarft bound to an antifolate
Analyse Crystal structure of aicarft bound to an antifolate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UZ0
- Type
- protein
- Length
- 2,355 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
- AMZ, 8US, MG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Bifunctional purine biosynthesis protein purh (EC 2.1.2.3, 3.5.4.10) | protein | 589 | 44% helix, 19% strand | P31939 |
| D | Bifunctional purine biosynthesis protein purh (EC 2.1.2.3, 3.5.4.10) | protein | 588 | 44% helix, 19% strand | P31939 |
Ligands and binding sites
- AMZ · Aminoimidazole 4-carboxamide ribonucleotide · ligand · 7 copies · chains A, B, C, D
- 8US · N-(6-fluoro-1-oxo-1,2-dihydroisoquinolin-7-yl)-5-[(3R)-3-hydroxypyrrolidin-1-yl]thiophene-2-sulfonamide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.80 | 0.83 | 83 | empty |
| 2 | 1003 | 0.79 | 0.80 | 98 | empty |
| 3 | 113 | 0.77 | 0.97 | 27 | empty |
| 4 | 888 | 0.77 | 0.80 | 89 | empty |
| 5 | 104 | 0.77 | 0.97 | 23 | empty |
Interfaces
5 interfaces between chains.
- C–D · 6441 Ų buried · 87 hydrogen bonds · protein-protein
- A–B · 6433 Ų buried · 94 hydrogen bonds · protein-protein
- B–C · 510 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 485 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 314 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5UZ0 · Crystal structure of AICARFT bound to an antifolate · 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 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 P31939
- Elsewhere: RCSB PDB 5UZ0 · PDBe 5UZ0 · UniProt P31939
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