Research workbench
Crystal structure of glycinamide ribonucleotide synthetase from thermus thermophilus HB8
Analyse Crystal structure of glycinamide ribonucleotide synthetase from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IP4
- Type
- protein
- Length
- 828 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
- Q5SK40
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoribosylamine--glycine ligase (EC 6.3.4.13) | protein | 414 | 32% helix, 27% strand | Q5SK40 |
Ligands and binding sites
- 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.75 | 0.78 | 75 | empty |
| 2 | 674 | 0.68 | 0.76 | 69 | SO4 |
| 3 | 138 | 0.37 | 0.72 | 24 | empty |
| 4 | 69 | 0.30 | 0.73 | 11 | empty |
| 5 | 67 | 0.27 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 646 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2IP4 · Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5SK40
- Elsewhere: RCSB PDB 2IP4 · PDBe 2IP4 · UniProt Q5SK40
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