MolNFT v1 · #46951 · protein + DNA
Fab ED10-DNA complex
2OK0 · 5'-D(*TP*C)-3': “Fab ED10-DNA complex”. X-ray diffraction, 3 pockets (best druggability 0.52). MolNFT v1 #46951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2OK0
- Type
- protein + DNA
- Length
- 437 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*C)-3'; Fab ED10 light chain; Fab ED10 heavy chain
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(*TP*C)-3' | dna | 2 | — | — |
| L | Fab ED10 light chain | protein | 219 | 6% helix, 51% strand | — |
| H | Fab ED10 heavy chain | protein | 216 | 7% helix, 52% strand | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.52 | 0.73 | 47 | empty |
| 2 | 118 | 0.46 | 0.78 | 28 | empty |
| 3 | 54 | 0.28 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1736 Ų buried · 17 hydrogen bonds · protein-protein
- D–H · 241 Ų buried · 2 hydrogen bonds · protein-nucleic
- D–L · 210 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2OK0 · Fab ED10-DNA complex · the same entry in another collection · chain L against L, 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 2OK0 · PDBe 2OK0
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