Research workbench
Crystal structure of pleckstrin homology domain (YP_926556.1) from shewanella amazonensis SB2B at 1.99 a resolution
Analyse Crystal structure of pleckstrin homology domain (YP_926556.1) from shewanella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HSA
- Type
- protein
- Length
- 585 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pleckstrin homology domain
- UniProt
- A1S3D0
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pleckstrin homology domain | protein | 125 | 26% helix, 40% strand | A1S3D0 |
| B | Pleckstrin homology domain | protein | 124 | 24% helix, 40% strand | A1S3D0 |
| C | Pleckstrin homology domain | protein | 112 | 26% helix, 42% strand | A1S3D0 |
| D | Pleckstrin homology domain | protein | 113 | 24% helix, 41% strand | A1S3D0 |
| E | Pleckstrin homology domain | protein | 111 | 24% helix, 43% strand | A1S3D0 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, E, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.69 | 0.80 | 52 | empty |
| 2 | 175 | 0.47 | 0.76 | 23 | PEG |
| 3 | 105 | 0.39 | 0.76 | 22 | empty |
| 4 | 118 | 0.38 | 0.74 | 22 | empty |
| 5 | 115 | 0.37 | 0.74 | 20 | GOL |
Interfaces
6 interfaces between chains.
- A–D · 1175 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 1144 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1107 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1087 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 928 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 68 modified (methylation, engineered).
Compared structures
- 3HSA · Crystal structure of pleckstrin homology domain (YP_926556.1) from SHEWANELLA AMAZONENSIS… · 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 A1S3D0
- Elsewhere: RCSB PDB 3HSA · PDBe 3HSA · UniProt A1S3D0
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