Research workbench
Crystal structure of cdpnpt in complex with thiolodiphosphate and (S)- benzodiazependione
Analyse Crystal structure of cdpnpt in complex with thiolodiphosphate and (S)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E0U
- Type
- protein
- Length
- 816 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic dipeptide N-prenyltransferase
- UniProt
- D1D8L6
- Ligands
- 0MV, PIS, NA
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclic dipeptide N-prenyltransferase | protein | 408 | 44% helix, 19% strand | D1D8L6 |
Ligands and binding sites
- 0MV · (3S)-3-(1H-indol-3-ylmethyl)-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione · ligand · 2 copies · chains A, B
- PIS · Trihydrogen thiodiphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
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 | 807 | 0.81 | 0.84 | 60 | 0MV, EDO, IMD |
| 2 | 725 | 0.81 | 0.84 | 68 | 0MV, PIS, IMD, EDO |
| 3 | 333 | 0.69 | 0.83 | 50 | empty |
| 4 | 233 | 0.68 | 0.85 | 30 | empty |
| 5 | 299 | 0.52 | 0.74 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 1027 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4E0U · Crystal structure of CdpNPT in complex with thiolodiphosphate and (S)-benzodiazependione · 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 D1D8L6
- Elsewhere: RCSB PDB 4E0U · PDBe 4E0U · UniProt D1D8L6
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