Research workbench
Crystal structure of the homodimeric bifunctional transformylase and cyclohydrolase enzyme avian atic in complex with aicar and xmp at 1.93 ångströms.
Analyse Crystal structure of the homodimeric bifunctional transformylase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M9N
- Type
- protein
- Length
- 1,180 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aicar transformylase-imp cyclohydrolase
- EC
- 2.1.2.3, 3.5.4.10
- UniProt
- P31335
- Ligands
- AMZ, XMP, K
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aicar transformylase-imp cyclohydrolase (EC 2.1.2.3, 3.5.4.10) | protein | 590 | 43% helix, 19% strand | P31335 |
Ligands and binding sites
- AMZ · Aminoimidazole 4-carboxamide ribonucleotide · ligand · 2 copies · chains A, B
- XMP · Xanthosine-5'-monophosphate · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.84 | 0.97 | 44 | empty |
| 2 | 897 | 0.76 | 0.79 | 72 | empty |
| 3 | 653 | 0.75 | 0.81 | 63 | AMZ |
| 4 | 577 | 0.74 | 0.81 | 67 | AMZ |
| 5 | 500 | 0.73 | 0.82 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 6115 Ų buried · 99 hydrogen bonds · protein-protein
Compared structures
- 1M9N · Crystal structure of the homodimeric bifunctional transformylase and cyclohydrolase… · the same entry in another collection · chain A against A, TM-score 1.00
- P31335 · 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 P31335
- Elsewhere: RCSB PDB 1M9N · PDBe 1M9N · UniProt P31335
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