MolNFT v1 · #64437 · protein + DNA
The catalytically inactive mutant MTH0212 (D151N) in complex with an 8 bp dsdna
3G38 · Exodeoxyribonuclease: “The catalytically inactive mutant MTH0212 (D151N) in complex with an 8 bp dsdna”. X-ray diffraction, 2 pockets (best druggability 0.47). MolNFT v1 #64437 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3G38
- Type
- protein + DNA
- Length
- 273 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease; 5'-D(*CP*CP*TP*GP*UP*GP*CP*GP*AP*T)-3'…
- EC
- 3.1.11.2
- UniProt
- O26314
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease (EC 3.1.11.2) | protein | 257 | 30% helix, 25% strand | O26314 |
| G | 5'-D(*CP*CP*TP*GP*UP*GP*CP*GP*AP*T)-3' | dna | 8 | — | — |
| K | 5'-D(*CP*GP*CP*GP*CP*AP*GP*GP*C)-3' | dna | 8 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.47 | 0.78 | 23 | empty |
| 2 | 66 | 0.46 | 0.83 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–K · 473 Ų buried · 12 hydrogen bonds · protein-nucleic
- G–K · 381 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–G · 365 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 3G38 · The catalytically inactive mutant Mth0212 (D151N) in complex with an 8 bp dsDNA · the same entry in another collection · chain A against A, TM-score 1.00
- O26314 · AlphaFold monomer V2.0 prediction for DNA uridine endonuclease (O26314) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O26314
- Elsewhere: RCSB PDB 3G38 · PDBe 3G38 · UniProt O26314
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