MolNFT v1 · #89827 · protein
Crystal structure of cdpnpt in its unbound state
4E0T · Cyclic dipeptide N-prenyltransferase: “Crystal structure of cdpnpt in its unbound state”. X-ray diffraction, 2 ligands (NA, CL), 20 pockets (best druggability 0.84). MolNFT v1 #89827 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4E0T
- Type
- protein
- Length
- 1,626 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic dipeptide N-prenyltransferase
- UniProt
- D1D8L6
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic dipeptide N-prenyltransferase | protein | 408 | 44% helix, 18% strand | D1D8L6 |
| B, C, D | Cyclic dipeptide N-prenyltransferase | protein | 406 | 43% helix, 18% strand | D1D8L6 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 12 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, C, D, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.84 | 0.84 | 108 | EDO |
| 2 | 663 | 0.74 | 0.80 | 45 | EDO |
| 3 | 661 | 0.74 | 0.80 | 49 | EDO |
| 4 | 649 | 0.74 | 0.80 | 52 | EDO |
| 5 | 602 | 0.73 | 0.80 | 46 | EDO |
Interfaces
6 interfaces between chains.
- A–C · 1098 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1091 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 986 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 984 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 635 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4E0T · Crystal structure of CdpNPT in its unbound state · 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 4E0T · PDBe 4E0T · UniProt D1D8L6
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