Research workbench
Synthetic Fab bound to marburg virus VP35 interferon inhibitory domain
Analyse Synthetic Fab bound to marburg virus VP35 interferon inhibitory domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OTC
- Type
- protein
- Length
- 553 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase cofactor VP35; Sfab H3 heavy chain; Sfab H3 light chain
- UniProt
- Q03039
- Ligands
- CL
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase cofactor VP35 | protein | 122 | 48% helix, 13% strand | Q03039 |
| H | Sfab H3 heavy chain | protein | 216 | 10% helix, 54% strand | — |
| L | Sfab H3 light chain | protein | 215 | 7% helix, 52% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.54 | 0.74 | 39 | empty |
| 2 | 51 | 0.52 | 0.88 | 21 | empty |
| 3 | 185 | 0.45 | 0.74 | 25 | empty |
| 4 | 143 | 0.41 | 0.74 | 18 | empty |
| 5 | 112 | 0.38 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1980 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 197 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 165 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6OTC · Synthetic Fab bound to Marburg virus VP35 interferon inhibitory domain · the same entry in another collection · chain A against A, 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
- Every structure of UniProt Q03039
- Elsewhere: RCSB PDB 6OTC · PDBe 6OTC · UniProt Q03039
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