Research workbench
Crystal structure of a DUF2853 member protein (JANN_4075) from jannaschia sp. CCS1 at 1.500 a resolution
Analyse Crystal structure of a DUF2853 member protein (JANN_4075) from jannaschia sp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PYQ
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q28JX0
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Uncharacterized protein | protein | 114 | 63% helix, 2% strand | Q28JX0 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.65 | 0.77 | 57 | empty |
| 2 | 129 | 0.48 | 0.79 | 30 | PG4 |
| 3 | 158 | 0.40 | 0.73 | 22 | empty |
| 4 | 92 | 0.37 | 0.76 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 400 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 303 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 291 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 283 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 2PYQ · Crystal structure of a duf2853 member protein (jann_4075) from jannaschia sp. ccs1 at… · the same entry in another collection · chain B against B, 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 Q28JX0
- Elsewhere: RCSB PDB 2PYQ · PDBe 2PYQ · UniProt Q28JX0
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