MolNFT v1 · #89688 · protein + DNA
Semet protelomerase tela covalently complexed with substrate DNA
4DWP: “Semet protelomerase tela covalently complexed with substrate DNA”. X-ray diffraction, 1 ligand (TMP), 3 pockets (best druggability 0.74). MolNFT v1 #89688 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DWP
- Type
- protein + DNA
- Length
- 350 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protelomerase; DNA (5'-D(*TP*TP*AP*CP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)- 3'); DNA (5'…
- UniProt
- Q7CWV1
- Ligands
- TMP
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protelomerase | protein | 319 | 57% helix, 8% strand | Q7CWV1 |
| C | DNA (5'-D(*TP*TP*AP*CP*AP*AP*TP*AP*AP*CP*AP*AP*TP*AP*T)- 3') | dna | 14 | — | — |
| D | DNA (5'- D(*CP*AP*TP*GP*AP*TP*AP*TP*TP*GP*TP*TP*AP*TP*TP*GP*TP*AP*A)-3') | dna | 17 | — | — |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.74 | 0.79 | 61 | TMP |
| 2 | 444 | 0.73 | 0.83 | 40 | empty |
| 3 | 52 | 0.29 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1229 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 960 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–D · 615 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 12 modified (engineered, phosphorylation).
Compared structures
- 4DWP · SeMet protelomerase tela covalently complexed with substrate DNA · 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 Q7CWV1
- Elsewhere: RCSB PDB 4DWP · PDBe 4DWP · UniProt Q7CWV1
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