MolNFT v1 · #12519 · protein
Crystal structure of purt-encoded glycinamide ribonucleotide transformylase complexed with mg-ATP
1KJ9 · Phosphoribosylglycinamide formyltransferase 2: “Crystal structure of purt-encoded glycinamide ribonucleotide transformylase complexed with mg-ATP”. X-ray diffraction, 4 ligands (ATP, MG, NA), 3 pockets (best druggability 0.84).…
- PDB
- 1KJ9
- Type
- protein
- Length
- 773 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylglycinamide formyltransferase 2
- EC
- 2.1.2.-
- UniProt
- P33221
- Ligands
- ATP, MG, NA, CL
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylglycinamide formyltransferase 2 (EC 2.1.2.-) | protein | 386 | 34% helix, 31% strand | P33221 |
| B | Phosphoribosylglycinamide formyltransferase 2 (EC 2.1.2.-) | protein | 387 | 33% helix, 30% strand | P33221 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.84 | 0.95 | 44 | empty |
| 2 | 941 | 0.77 | 0.80 | 72 | MG, ATP |
| 3 | 712 | 0.74 | 0.80 | 57 | MG, CL, ATP, EDO |
Interfaces
1 interface between chains.
- A–B · 2456 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 1KJ9 · Crystal structure of purt-encoded glycinamide ribonucleotide transformylase complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P33221 · AlphaFold monomer V2.0 prediction for formate-dependent phosphoribosylglycinamide… · a predicted model of the same protein · chain B 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 P33221
- Elsewhere: RCSB PDB 1KJ9 · PDBe 1KJ9 · UniProt P33221
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