MolNFT v1 · #12523 · protein
Crystal structure of glycinamide ribonucleotide transformylase in complex with mg-amppcp
1KJI · Phosphoribosylglycinamide formyltransferase 2: “Crystal structure of glycinamide ribonucleotide transformylase in complex with mg-amppcp”. X-ray diffraction, 4 ligands (ACP, MG, NA), 5 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 1KJI
- Type
- protein
- Length
- 778 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
- ACP, MG, NA, CL
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoribosylglycinamide formyltransferase 2 (EC 2.1.2.-) | protein | 389 | 34% helix, 31% strand | P33221 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · chains A
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.82 | 0.96 | 36 | empty |
| 2 | 878 | 0.75 | 0.79 | 68 | MG, ACP |
| 3 | 822 | 0.75 | 0.79 | 61 | MG, ACP |
| 4 | 52 | 0.68 | 0.96 | 13 | empty |
| 5 | 54 | 0.27 | 0.74 | 18 | NA, MPO |
Interfaces
1 interface between chains.
- A–B · 2435 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 1KJI · Crystal structure of glycinamide ribonucleotide transformylase in complex with Mg-AMPPCP · 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 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 P33221
- Elsewhere: RCSB PDB 1KJI · PDBe 1KJI · UniProt P33221
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