Research workbench
Crystal structure of a cupin protein (TM1459) in osmium (os)- substituted form II
Analyse Crystal structure of a cupin protein (TM1459) in osmium (os)- substituted form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WSF
- Type
- protein
- Length
- 445 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein TM1459
- UniProt
- Q9X1H0
- Ligands
- OS
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Uncharacterized protein TM1459 | protein | 114 | 5% helix, 61% strand | Q9X1H0 |
| C | Uncharacterized protein TM1459 | protein | 108 | 6% helix, 56% strand | Q9X1H0 |
| D | Uncharacterized protein TM1459 | protein | 109 | 6% helix, 60% strand | Q9X1H0 |
Ligands and binding sites
- OS · Osmium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.74 | 0.77 | 88 | empty |
| 2 | 125 | 0.46 | 0.78 | 24 | empty |
| 3 | 107 | 0.43 | 0.77 | 21 | empty |
| 4 | 116 | 0.38 | 0.74 | 24 | empty |
| 5 | 66 | 0.32 | 0.75 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1867 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1840 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 290 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 88 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 5WSF · Crystal structure of a cupin protein (tm1459) in osmium (Os)-substituted form II · 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 Q9X1H0
- Elsewhere: RCSB PDB 5WSF · PDBe 5WSF · UniProt Q9X1H0
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