MolNFT v1 · #12531 · protein
Crystal structure of glycinamide ribonucleotide transformylase in complex with mg-ADP
1KJQ · Phosphoribosylglycinamide formyltransferase 2: “Crystal structure of glycinamide ribonucleotide transformylase in complex with mg-ADP”. X-ray diffraction, 4 ligands (ADP, MG, NA), 5 pockets (best druggability 0.83). MolNFT v1 #12531…
- PDB
- 1KJQ
- 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
- ADP, MG, NA, CL
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoribosylglycinamide formyltransferase 2 (EC 2.1.2.-) | protein | 388 | 35% helix, 31% strand | P33221 |
| B | Phosphoribosylglycinamide formyltransferase 2 (EC 2.1.2.-) | protein | 385 | 34% helix, 30% strand | P33221 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 15 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.83 | 0.95 | 42 | EDO |
| 2 | 843 | 0.74 | 0.78 | 64 | MG, ADP |
| 3 | 751 | 0.69 | 0.76 | 56 | MG, ADP, EDO |
| 4 | 57 | 0.26 | 0.73 | 17 | MPO, NA |
| 5 | 52 | 0.26 | 0.73 | 13 | EDO |
Interfaces
1 interface between chains.
- A–B · 2456 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 1KJQ · Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-ADP · 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 1KJQ · PDBe 1KJQ · UniProt P33221
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