Research workbench
Crystal structure of a DUF1989 family protein (SPO0365) from silicibacter pomeroyi dss-3 at 1.60 a resolution
Analyse Crystal structure of a DUF1989 family protein (SPO0365) from silicibacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DI4
- Type
- protein
- Length
- 554 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein DUF1989
- UniProt
- Q5LXE3
- Ligands
- ZN, CL, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein DUF1989 | protein | 281 | 19% helix, 31% strand | Q5LXE3 |
| B | Uncharacterized protein DUF1989 | protein | 273 | 20% helix, 31% strand | Q5LXE3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · chains A
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 | 402 | 0.80 | 0.88 | 36 | empty |
| 2 | 278 | 0.61 | 0.79 | 40 | CL |
| 3 | 306 | 0.60 | 0.78 | 36 | SO4 |
| 4 | 70 | 0.41 | 0.80 | 18 | empty |
| 5 | 74 | 0.40 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4268 Ų buried · 67 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 3DI4 · Crystal structure of a duf1989 family protein (spo0365) from silicibacter pomeroyi dss-3… · 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 Q5LXE3
- Elsewhere: RCSB PDB 3DI4 · PDBe 3DI4 · UniProt Q5LXE3
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