Research workbench
MTH0212 (wt) in complex with a 7BP dsdna
Analyse MTH0212 (wt) in complex with a 7BP dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G4T
- Type
- protein + DNA
- Length
- 523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease; 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3'…
- EC
- 3.1.11.2
- UniProt
- O26314
- Ligands
- MG, PO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease (EC 3.1.11.2) | protein | 254 | 30% helix, 27% strand | O26314 |
| B | Exodeoxyribonuclease (EC 3.1.11.2) | protein | 255 | 30% helix, 25% strand | O26314 |
| H | 5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3' | dna | 7 | — | — |
| I | 5'-D(*CP*G*TP*AP*CP*TP*AP*CP*G)-3' | dna | 7 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, H, B, I
- PO4 · Phosphate ion · ion · 3 copies · chains A, H, B, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.71 | 0.91 | 28 | empty |
| 2 | 153 | 0.53 | 0.80 | 31 | PO4 |
| 3 | 156 | 0.52 | 0.79 | 25 | PO4 |
| 4 | 82 | 0.34 | 0.75 | 15 | empty |
| 5 | 74 | 0.32 | 0.75 | 11 | empty |
Interfaces
6 interfaces between chains.
- B–H · 499 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–I · 483 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–I · 361 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–H · 357 Ų buried · 5 hydrogen bonds · protein-nucleic
- H–I · 323 Ų buried · 29 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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 3G4T · PDBe 3G4T · UniProt O26314
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.