Research workbench
Crystal structure of hypothetical protein PH1004 from pyrococcus horikoshii OT3
Analyse Crystal structure of hypothetical protein PH1004 from pyrococcus horikoshii OT3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GJU
- Type
- protein
- Length
- 1,008 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 252AA long hypothetical protein
- UniProt
- O58732
- Ligands
- NA, PO4
- Pockets
- 11 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 252AA long hypothetical protein | protein | 252 | 38% helix, 23% strand | O58732 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 7 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.51 | 0.74 | 34 | empty |
| 2 | 148 | 0.45 | 0.76 | 23 | empty |
| 3 | 158 | 0.45 | 0.75 | 21 | empty |
| 4 | 103 | 0.42 | 0.77 | 23 | PO4 |
| 5 | 95 | 0.42 | 0.78 | 23 | PO4 |
Interfaces
3 interfaces between chains.
- A–B · 987 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 282 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 169 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2GJU · Crystal structure of hypothetical protein PH1004 from Pyrococcus horikoshii OT3 · 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 O58732
- Elsewhere: RCSB PDB 2GJU · PDBe 2GJU · UniProt O58732
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