Research workbench
Crystal structure of bacterial pnkp-C/HEN1-N heterodimer
Analyse Crystal structure of bacterial pnkp-C/HEN1-N heterodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E6N
- Type
- protein
- Length
- 1,250 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallophosphoesterase; Methyltransferase type 12
- UniProt
- A3DJ38, A3DJ37
- Ligands
- AMP, MG
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Metallophosphoesterase | protein | 407 | 45% helix, 17% strand | A3DJ38 |
| B, D | Methyltransferase type 12 | protein | 218 | 42% helix, 28% strand | A3DJ37 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.77 | 0.81 | 60 | MG, AMP |
| 2 | 699 | 0.76 | 0.81 | 57 | MG, AMP |
| 3 | 143 | 0.50 | 0.79 | 22 | empty |
| 4 | 127 | 0.41 | 0.75 | 15 | empty |
| 5 | 92 | 0.40 | 0.78 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2127 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2113 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 202 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 86 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4E6N · 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 4E6N · PDBe 4E6N · UniProt A3DJ38 · UniProt A3DJ37
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