MolNFT v1 · #47895 · protein
Crystal structure of PH0725 from pyrococcus horikoshii OT3
2PCI · Probable diphthine synthase: “Crystal structure of PH0725 from pyrococcus horikoshii OT3”. X-ray diffraction, 1 ligand (SAH), 6 pockets (best druggability 0.74). MolNFT v1 #47895 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2PCI
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable diphthine synthase
- EC
- 2.1.1.98
- UniProt
- O58456
- Ligands
- SAH
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable diphthine synthase (EC 2.1.1.98) | protein | 265 | 39% helix, 23% strand | O58456 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.74 | 0.83 | 49 | empty |
| 2 | 344 | 0.71 | 0.84 | 48 | SAH |
| 3 | 126 | 0.41 | 0.75 | 20 | empty |
| 4 | 88 | 0.37 | 0.76 | 20 | empty |
| 5 | 93 | 0.36 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2600 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
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 O58456
- Elsewhere: RCSB PDB 2PCI · PDBe 2PCI · UniProt O58456
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