Research workbench
Crystal structure of phosphoribosyl diphosphate synthase from methanocaldococcus jannaschii
Analyse Crystal structure of phosphoribosyl diphosphate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U9Y
- Type
- protein
- Length
- 1,096 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose-phosphate pyrophosphokinase
- EC
- 2.7.6.1
- UniProt
- Q58761
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ribose-phosphate pyrophosphokinase (EC 2.7.6.1) | protein | 274 | 33% helix, 24% strand | Q58761 |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.76 | 0.79 | 107 | empty |
| 2 | 1118 | 0.76 | 0.78 | 100 | empty |
| 3 | 247 | 0.69 | 0.85 | 48 | empty |
| 4 | 270 | 0.68 | 0.84 | 47 | empty |
| 5 | 278 | 0.66 | 0.82 | 53 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1870 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1858 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1289 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1275 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 1U9Y · Crystal Structure of Phosphoribosyl Diphosphate Synthase from Methanocaldococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58761 · AlphaFold monomer V2.0 prediction for ribose-phosphate pyrophosphokinase (Q58761) · a predicted model of the same protein · chain A 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 Q58761
- Elsewhere: RCSB PDB 1U9Y · PDBe 1U9Y · UniProt Q58761
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