Research workbench
Crystal structure of an imp biosynthesis protein purp from thermococcus kodakaraensis
Analyse Crystal structure of an imp biosynthesis protein purp from thermococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PBZ
- Type
- protein
- Length
- 879 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- EC
- 6.3.4.-
- UniProt
- Q5JD28
- Ligands
- ATP
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hypothetical protein (EC 6.3.4.-) | protein | 293 | 28% helix, 25% strand | Q5JD28 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.87 | 0.88 | 122 | ATP |
| 2 | 149 | 0.80 | 0.97 | 42 | empty |
| 3 | 486 | 0.76 | 0.84 | 69 | empty |
| 4 | 55 | 0.26 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1800 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1772 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1744 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 2PBZ · Crystal structure of an IMP biosynthesis protein PurP from Thermococcus kodakaraensis · 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 Q5JD28
- Elsewhere: RCSB PDB 2PBZ · PDBe 2PBZ · UniProt Q5JD28
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