MolNFT v1 · #35728 · protein
Structural study of project id PH0725 from pyrococcus horikoshii OT3 (L3M)
2EK3 · Diphthine synthase: “Structural study of project id PH0725 from pyrococcus horikoshii OT3 (L3M)”. X-ray diffraction, 2 ligands (SAH, NA), 7 pockets (best druggability 0.74). MolNFT v1 #35728 on GenesisL1: 3D structure, binding sites…
- PDB
- 2EK3
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphthine synthase
- EC
- 2.1.1.98
- UniProt
- O58456
- Ligands
- SAH, NA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Diphthine synthase (EC 2.1.1.98) | protein | 264 | 39% helix, 21% strand | O58456 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.74 | 0.82 | 50 | empty |
| 2 | 402 | 0.73 | 0.84 | 61 | SAH |
| 3 | 155 | 0.42 | 0.74 | 21 | empty |
| 4 | 95 | 0.38 | 0.76 | 16 | empty |
| 5 | 81 | 0.35 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2557 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2EK3 · Structural study of Project ID PH0725 from Pyrococcus horikoshii OT3 (L3M) · the same entry in another collection · chain B against B, TM-score 1.00
- O58456 · AlphaFold monomer V2.0 prediction for diphthine synthase (O58456) · a predicted model of the same protein · chain B 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 O58456
- Elsewhere: RCSB PDB 2EK3 · PDBe 2EK3 · UniProt O58456
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