Research workbench
Crystal structure of CdpNPT in complex with harmol
Analyse Crystal structure of CdpNPT in complex with harmol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XVJ
- Type
- protein
- Length
- 1,584 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Neosartorya fumigata
- Molecule
- Cyclic dipeptide N-prenyltransferase
- UniProt
- D1D8L6
- Ligands
- HFI, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.4 · 3 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cyclic dipeptide N-prenyltransferase | protein | 404 | 45% helix, 19% strand | D1D8L6 |
| B | Cyclic dipeptide N-prenyltransferase | protein | 399 | 45% helix, 18% strand | D1D8L6 |
| D | Cyclic dipeptide N-prenyltransferase | protein | 377 | 44% helix, 19% strand | D1D8L6 |
Ligands and binding sites
- HFI · 1-methyl-9~{H}-pyrido[3,4-b]indol-7-ol · ligand · chains D
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.79 | 0.83 | 58 | empty |
| 2 | 598 | 0.79 | 0.85 | 77 | PO4 |
| 3 | 771 | 0.79 | 0.82 | 56 | empty |
| 4 | 685 | 0.78 | 0.83 | 48 | empty |
| 5 | 492 | 0.77 | 0.85 | 77 | PO4 |
Interfaces
6 interfaces between chains.
- A–C · 947 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 593 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 516 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 399 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 279 Ų buried · 1 hydrogen bond · protein-protein
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 D1D8L6
- Elsewhere: RCSB PDB 7XVJ · PDBe 7XVJ · UniProt D1D8L6
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