Research workbench
Structure of OKRAI/DNA complex
Analyse Structure of OKRAI/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ODH
- Type
- protein + DNA
- Length
- 822 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Okrai endonuclease; DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3')
- Ligands
- CA
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Okrai endonuclease | protein | 194 | 29% helix, 27% strand | — |
| B | Okrai endonuclease | protein | 192 | 29% helix, 31% strand | — |
| C, D, G, H | DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3') | dna | 12 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, D, B, C, E, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.71 | 0.76 | 64 | empty |
| 2 | 217 | 0.66 | 0.85 | 24 | CA |
| 3 | 239 | 0.61 | 0.81 | 26 | empty |
| 4 | 317 | 0.55 | 0.75 | 29 | empty |
| 5 | 276 | 0.54 | 0.76 | 24 | empty |
Interfaces
15 interfaces between chains.
- E–F · 1324 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1218 Ų buried · 7 hydrogen bonds · protein-protein
- E–H · 852 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 852 Ų buried · 14 hydrogen bonds · protein-nucleic
- F–G · 810 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 3ODH · Structure of OkrAI/DNA complex · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 3ODH · PDBe 3ODH
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.