Research workbench
MTH0212 in complex with two DNA helices
Analyse MTH0212 in complex with two DNA helices in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GA6
- Type
- protein + DNA
- Length
- 553 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exodeoxyribonuclease; 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*C)-3'…
- EC
- 3.1.11.2
- UniProt
- O26314
- Ligands
- NA, PO4
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exodeoxyribonuclease (EC 3.1.11.2) | protein | 254 | 27% helix, 28% strand | O26314 |
| B | Exodeoxyribonuclease (EC 3.1.11.2) | protein | 255 | 28% helix, 25% strand | O26314 |
| F | 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*C)-3' | dna | 11 | — | — |
| G | 5'-D(*GP*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3' | dna | 10 | — | — |
| H | 5'-D(*GP*CP*TP*GP*CP*GP*CP*AP*GP*GP*GP*C)-3' | dna | 11 | — | — |
| D | 5'-D(*GP*CP*CP*CP*TP*GP*UP*GP*CP*AP*GP*C)-3' | dna | 12 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 19 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.60 | 0.84 | 26 | GOL |
| 2 | 215 | 0.55 | 0.78 | 29 | empty |
| 3 | 165 | 0.54 | 0.80 | 29 | GOL |
| 4 | 287 | 0.51 | 0.74 | 20 | empty |
| 5 | 52 | 0.43 | 0.84 | 17 | empty |
Interfaces
7 interfaces between chains.
- F–D · 542 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- G–H · 489 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- B–H · 477 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–F · 403 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–B · 383 Ų buried · 6 hydrogen bonds · protein-protein
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 3GA6 · PDBe 3GA6 · UniProt O26314
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.