Research workbench
SP140 phd-bromodomain complex with scfv
Analyse SP140 phd-bromodomain complex with scfv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G8R
- Type
- protein
- Length
- 391 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-chain variable fragment; Nuclear body protein SP140
- UniProt
- Q13342
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-chain variable fragment | protein | 227 | 4% helix, 52% strand | — |
| B | Nuclear body protein SP140 | protein | 164 | 46% helix, 4% strand | Q13342 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 148 | 0.54 | 0.81 | 28 | empty |
| 2 | 68 | 0.50 | 0.85 | 23 | empty |
| 3 | 79 | 0.32 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 930 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 Q13342
- Elsewhere: RCSB PDB 6G8R · PDBe 6G8R · UniProt Q13342
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