Research workbench
Structures of apo and complexed escherichia COLI glycinamide ribonucleotide transformylase
Analyse Structures of apo and complexed escherichia COLI glycinamide ribonucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CDE
- Type
- protein
- Length
- 836 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosyl-glycinamide formyltransferase
- EC
- 2.1.2.2
- UniProt
- P08179
- Ligands
- GAR, DZF
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Phosphoribosyl-glycinamide formyltransferase (EC 2.1.2.2) | protein | 209 | 36% helix, 25% strand | P08179 |
Ligands and binding sites
- GAR · Glycinamide ribonucleotide · ligand · 4 copies · chains A, B, C, D
- DZF · 5-deazafolic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.65 | 0.80 | 43 | GAR, DZF |
| 2 | 346 | 0.65 | 0.80 | 39 | GAR, DZF |
| 3 | 352 | 0.65 | 0.80 | 40 | GAR, DZF |
| 4 | 336 | 0.64 | 0.80 | 38 | GAR, DZF |
Interfaces
2 interfaces between chains.
- B–C · 135 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1CDE · Structures of apo and complexed escherichia COLI glycinamide ribonucleotide transformylase · the same entry in another collection · chain D against D, TM-score 1.00
- P08179 · AlphaFold monomer V2.0 prediction for phosphoribosylglycinamide formyltransferase (P08179) · a predicted model of the same protein · chain D 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 P08179
- Elsewhere: RCSB PDB 1CDE · PDBe 1CDE · UniProt P08179
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.