Research workbench
Human glycinamide ribonucleotide transformylase domain at pH 8.5
Analyse Human glycinamide ribonucleotide transformylase domain at pH 8.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MEJ
- Type
- protein
- Length
- 603 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylglycinamide formyltransferase
- EC
- 2.1.2.2
- UniProt
- P22102
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) | protein | 201 | 36% helix, 24% strand | P22102 |
Ligands and binding sites
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 | 724 | 0.72 | 0.78 | 68 | GOL |
| 2 | 678 | 0.70 | 0.78 | 61 | GOL |
| 3 | 437 | 0.65 | 0.78 | 45 | PO4 |
| 4 | 398 | 0.61 | 0.76 | 46 | empty |
| 5 | 123 | 0.37 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 694 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 276 Ų buried · 3 hydrogen bonds · protein-protein
- B–A · 94 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1MEJ · Human Glycinamide Ribonucleotide Transformylase domain at pH 8.5 · the same entry in another collection · chain B against B, TM-score 1.00
- P22102 · AlphaFold monomer V2.0 prediction for trifunctional purine biosynthetic protein… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P22102
- Elsewhere: RCSB PDB 1MEJ · PDBe 1MEJ · UniProt P22102
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