Research workbench
Structure of escherichia COLI purt-encoded glycinamide ribonucleotide transformylase complexed with mg and amppnp
Analyse Structure of escherichia COLI purt-encoded glycinamide ribonucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EYZ
- 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
- ANP, MG, NA, CL
- Pockets
- 3 · best druggability 0.84
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
- ANP · Phosphoaminophosphonic acid-adenylate ester · 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 · chains A
- 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 | 252 | 0.84 | 0.96 | 42 | empty |
| 2 | 928 | 0.77 | 0.80 | 71 | MG, ANP |
| 3 | 787 | 0.75 | 0.79 | 62 | MG, ANP |
Interfaces
1 interface between chains.
- A–B · 2444 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 1EYZ · Structure of escherichia COLI purt-encoded glycinamide ribonucleotide transformylase… · 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 1EYZ · PDBe 1EYZ · UniProt P33221
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