Research workbench
Crystal structure of a DUF1696 family protein with a pleckstrin- homology domain (SHEW_0819) from shewanella loihica pv-4 at 2.00 a resolution
Analyse Crystal structure of a DUF1696 family protein with a pleckstrin- homology… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DCX
- Type
- protein
- Length
- 561 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein of unknown function (DUF1696) with pleckstrin- homology domains
- UniProt
- A3QB43
- Ligands
- CL
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein of unknown function (DUF1696) with pleckstrin- homology domains | protein | 117 | 22% helix, 44% strand | A3QB43 |
| B, D | Protein of unknown function (DUF1696) with pleckstrin- homology domains | protein | 113 | 26% helix, 45% strand | A3QB43 |
| C | Protein of unknown function (DUF1696) with pleckstrin- homology domains | protein | 115 | 23% helix, 43% strand | A3QB43 |
| E | Protein of unknown function (DUF1696) with pleckstrin- homology domains | protein | 103 | 25% helix, 43% strand | A3QB43 |
Ligands and binding sites
- CL · Chloride ion · ion · chains B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 7 copies · chains A, E, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.63 | 0.76 | 61 | MPD |
| 2 | 82 | 0.58 | 0.87 | 17 | MPD |
| 3 | 93 | 0.51 | 0.83 | 18 | MPD |
| 4 | 151 | 0.46 | 0.76 | 24 | empty |
| 5 | 164 | 0.44 | 0.74 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–E · 1039 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 991 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 990 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 945 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 886 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3DCX · Crystal structure of a duf1696 family protein with a pleckstrin-homology 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 A3QB43
- Elsewhere: RCSB PDB 3DCX · PDBe 3DCX · UniProt A3QB43
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