MolNFT v1 · #138776 · protein
Crystal structure of dnde G21/24K mutant involved in DNA phosphorothioation
5WTU · DNA sulfur modification protein dnde: “Crystal structure of dnde G21/24K mutant involved in DNA phosphorothioation”. X-ray diffraction, 5 pockets (best druggability 0.87). MolNFT v1 #138776 on GenesisL1: 3D structure, binding sites…
- PDB
- 5WTU
- Type
- protein
- Length
- 388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA sulfur modification protein dnde
- UniProt
- A0A0N8J336
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA sulfur modification protein dnde | protein | 104 | 57% helix, 6% strand | A0A0N8J336 |
| B | DNA sulfur modification protein dnde | protein | 91 | 62% helix, 7% strand | A0A0N8J336 |
| C | DNA sulfur modification protein dnde | protein | 98 | 63% helix, 6% strand | A0A0N8J336 |
| D | DNA sulfur modification protein dnde | protein | 95 | 62% helix, 6% strand | A0A0N8J336 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.87 | 0.92 | 83 | empty |
| 2 | 85 | 0.49 | 0.82 | 24 | empty |
| 3 | 75 | 0.46 | 0.82 | 15 | empty |
| 4 | 135 | 0.42 | 0.75 | 24 | empty |
| 5 | 76 | 0.33 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–C · 769 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 597 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 428 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 372 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 353 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5WTU · Crystal structure of DndE G21/24K mutant involved in DNA phosphorothioation · 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 A0A0N8J336
- Elsewhere: RCSB PDB 5WTU · PDBe 5WTU · UniProt A0A0N8J336
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