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Xchem group deposition -- crystal structure of the second bromodomain of pleckstrin homology domain interacting protein (phip) in complex with FMO3D000185A (space group P212121)
Analyse Xchem group deposition -- crystal structure of the second bromodomain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5S8Q
- Type
- protein
- Length
- 243 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PH-interacting protein
- UniProt
- Q8WWQ0
- Ligands
- XLY, CA
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PH-interacting protein | protein | 124 | 69% helix, 0% strand | Q8WWQ0 |
| B | PH-interacting protein | protein | 119 | 69% helix, 0% strand | Q8WWQ0 |
Ligands and binding sites
- XLY · (3R)-3-methyl-1,2,3,4-tetrahydro-5H-1,4-benzodiazepin-5-one · ligand · chains B
- CA · Calcium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.74 | 0.81 | 70 | XLY |
| 2 | 86 | 0.46 | 0.81 | 18 | EDO |
Interfaces
1 interface between chains.
- A–B · 519 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5S8Q · XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin… · 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 Q8WWQ0
- Elsewhere: RCSB PDB 5S8Q · PDBe 5S8Q · UniProt Q8WWQ0
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