Research workbench
Crystal structure of probable phosphoribosylglycinamide formyl transferase from pyrococcus horikoshii OT3 complexed with ADP
Analyse Crystal structure of probable phosphoribosylglycinamide formyl transferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DWC
- Type
- protein
- Length
- 815 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 433AA long hypothetical phosphoribosylglycinamide formyl transferase
- EC
- 2.1.2.-
- UniProt
- O58056
- Ligands
- ADP, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 433AA long hypothetical phosphoribosylglycinamide formyl transferase (EC 2.1.2.-) | protein | 406 | 32% helix, 30% strand | O58056 |
| B | 433AA long hypothetical phosphoribosylglycinamide formyl transferase (EC 2.1.2.-) | protein | 409 | 32% helix, 30% strand | O58056 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.78 | 0.97 | 37 | empty |
| 2 | 763 | 0.71 | 0.77 | 65 | SO4, ADP |
| 3 | 725 | 0.69 | 0.77 | 64 | SO4, ADP |
| 4 | 56 | 0.41 | 0.81 | 15 | empty |
| 5 | 54 | 0.41 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2779 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 2DWC · Crystal structure of Probable phosphoribosylglycinamide formyl transferase from… · the same entry in another collection · chain A against A, TM-score 1.00
- O58056 · 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 O58056
- Elsewhere: RCSB PDB 2DWC · PDBe 2DWC · UniProt O58056
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