MolNFT v1 · #89513 · protein
Crystal structure of bacterial pnkp-C/HEN1-N heterodimer
4DRF · Metallophosphoesterase: “Crystal structure of bacterial pnkp-C/HEN1-N heterodimer”. X-ray diffraction, 14 pockets (best druggability 0.77). MolNFT v1 #89513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DRF
- Type
- protein
- Length
- 1,228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallophosphoesterase; Methyltransferase type 12
- UniProt
- A3DJ38, A3DJ37
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Metallophosphoesterase | protein | 408 | 45% helix, 18% strand | A3DJ38 |
| B, D | Methyltransferase type 12 | protein | 206 | 32% helix, 30% strand | A3DJ37 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.77 | 0.80 | 79 | empty |
| 2 | 877 | 0.76 | 0.80 | 86 | empty |
| 3 | 63 | 0.62 | 0.91 | 22 | empty |
| 4 | 66 | 0.49 | 0.84 | 23 | empty |
| 5 | 143 | 0.48 | 0.78 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2074 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2053 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 195 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 157 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4DRF · Crystal Structure of Bacterial Pnkp-C/Hen1-N Heterodimer · 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 A3DJ38
- Every structure of UniProt A3DJ37
- Elsewhere: RCSB PDB 4DRF · PDBe 4DRF · UniProt A3DJ38 · UniProt A3DJ37
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.