Research workbench
Crystal structure of PH0832 from pyrococcus horikoshii OT3
Analyse Crystal structure of PH0832 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
- 2P9X
- Type
- protein
- Length
- 389 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein PH0832
- UniProt
- O58562
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Hypothetical protein PH0832 | protein | 98 | 78% helix, 0% strand | O58562 |
| B | Hypothetical protein PH0832 | protein | 95 | 79% helix, 0% strand | O58562 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.45 | 0.77 | 22 | ZN |
| 2 | 124 | 0.44 | 0.77 | 22 | empty |
| 3 | 58 | 0.31 | 0.75 | 11 | empty |
| 4 | 58 | 0.30 | 0.75 | 11 | empty |
Interfaces
6 interfaces between chains.
- A–D · 791 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 791 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 358 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 352 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2P9X · Crystal structure of PH0832 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 O58562
- Elsewhere: RCSB PDB 2P9X · PDBe 2P9X · UniProt O58562
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