MolNFT v1 · #19208 · protein
The crystal structure of the formiminotransferase domain of formiminotransferase-cyclodeaminase.
1QD1: “The crystal structure of the formiminotransferase domain of formiminotransferase-cyclodeaminase.”. X-ray diffraction, 1 ligand (FON), 4 pockets (best druggability 0.78). MolNFT v1 #19208 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1QD1
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formiminotransferase-cyclodeaminase
- EC
- 2.1.2.5
- UniProt
- P53603
- Ligands
- FON
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formiminotransferase-cyclodeaminase (EC 2.1.2.5) | protein | 319 | 41% helix, 24% strand | P53603 |
| B | Formiminotransferase-cyclodeaminase (EC 2.1.2.5) | protein | 325 | 40% helix, 25% strand | P53603 |
Ligands and binding sites
- FON · N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.78 | 0.84 | 76 | FON, GOL |
| 2 | 581 | 0.77 | 0.83 | 72 | FON, GOL |
| 3 | 463 | 0.66 | 0.79 | 39 | empty |
| 4 | 300 | 0.61 | 0.79 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 1053 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1QD1 · The crystal structure of the formiminotransferase domain of… · the same entry in another collection · chain A against A, TM-score 1.00
- P53603 · AlphaFold monomer V2.0 prediction for formimidoyltransferase- cyclodeaminase (P53603) · a predicted model of the same protein · chain A 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 P53603
- Elsewhere: RCSB PDB 1QD1 · PDBe 1QD1 · UniProt P53603
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