Research workbench
Crystal structure of a DUF1989 family protein (TM1040_0329) from silicibacter sp. TM1040 at 1.35 a resolution
Analyse Crystal structure of a DUF1989 family protein (TM1040_0329) from silicibacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SIY
- Type
- protein
- Length
- 923 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DUF1989 family protein
- UniProt
- Q1GJV4
- Ligands
- ZN, MG, CL
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | DUF1989 family protein | protein | 231 | 15% helix, 30% strand | Q1GJV4 |
| D | DUF1989 family protein | protein | 230 | 16% helix, 31% strand | Q1GJV4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains C
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.77 | 0.80 | 89 | empty |
| 2 | 372 | 0.63 | 0.79 | 36 | empty |
| 3 | 279 | 0.56 | 0.77 | 41 | empty |
| 4 | 268 | 0.55 | 0.77 | 38 | empty |
| 5 | 62 | 0.54 | 0.88 | 22 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1873 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1863 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 341 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 178 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3SIY · Crystal structure of a DUF1989 family protein (TM1040_0329) from SILICIBACTER SP. TM1040… · 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 Q1GJV4
- Elsewhere: RCSB PDB 3SIY · PDBe 3SIY · UniProt Q1GJV4
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