MolNFT v1 · #11603 · protein
Crystal structure of a nudix protein from pyrobaculum aerophilum reveals a dimer with intertwined beta sheets
1JRK · Nudix homolog: “Crystal structure of a nudix protein from pyrobaculum aerophilum reveals a dimer with intertwined beta sheets”. X-ray diffraction, 13 pockets (best druggability 0.79). MolNFT v1 #11603 on GenesisL1: 3D structure…
- PDB
- 1JRK
- Type
- protein
- Length
- 593 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nudix homolog
- UniProt
- Q8ZTD8
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nudix homolog | protein | 148 | 26% helix, 38% strand | Q8ZTD8 |
| B | Nudix homolog | protein | 147 | 24% helix, 39% strand | Q8ZTD8 |
| D | Nudix homolog | protein | 150 | 27% helix, 39% strand | Q8ZTD8 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.79 | 0.81 | 70 | MPD |
| 2 | 135 | 0.60 | 0.85 | 27 | empty |
| 3 | 131 | 0.60 | 0.84 | 25 | empty |
| 4 | 132 | 0.57 | 0.83 | 24 | MPD |
| 5 | 171 | 0.55 | 0.80 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1608 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1590 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 693 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 556 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1JRK · Crystal Structure of a Nudix Protein from Pyrobaculum aerophilum Reveals a Dimer with… · 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 Q8ZTD8
- Elsewhere: RCSB PDB 1JRK · PDBe 1JRK · UniProt Q8ZTD8
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