Research workbench
Crystal structure of phosphoribosylamine--glycine ligase (TM1250) from thermotoga maritima at 2.30 a resolution
Analyse Crystal structure of phosphoribosylamine--glycine ligase (TM1250) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VKZ
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoribosylamine--glycine ligase
- EC
- 6.3.4.13
- UniProt
- Q9X0X7
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoribosylamine--glycine ligase (EC 6.3.4.13) | protein | 391 | 30% helix, 29% strand | Q9X0X7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.73 | 0.78 | 77 | empty |
| 2 | 829 | 0.73 | 0.78 | 78 | EDO |
| 3 | 240 | 0.47 | 0.73 | 34 | empty |
| 4 | 200 | 0.44 | 0.73 | 30 | empty |
| 5 | 83 | 0.32 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 372 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 1VKZ · Crystal structure of Phosphoribosylamine--glycine ligase (TM1250) from Thermotoga… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X0X7 · AlphaFold monomer V2.0 prediction for phosphoribosylamine--glycine ligase (Q9X0X7) · a predicted model of the same protein · chain A 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 Q9X0X7
- Elsewhere: RCSB PDB 1VKZ · PDBe 1VKZ · UniProt Q9X0X7
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