Research workbench
Crystal structure of pyrococcus horikoshii DPH2 with 4FE-4S cluster and SAM
Analyse Crystal structure of pyrococcus horikoshii DPH2 with 4FE-4S cluster and SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BXL
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase
- EC
- 2.5.1.108
- UniProt
- O58832
- Ligands
- SAM, SF4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase (EC 2.5.1.108) | protein | 339 | 32% helix, 21% strand | O58832 |
| B | 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase (EC 2.5.1.108) | protein | 337 | 32% helix, 20% strand | O58832 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.76 | 0.83 | 78 | SAM, SF4 |
| 2 | 363 | 0.65 | 0.79 | 47 | SAM, SF4 |
| 3 | 56 | 0.40 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1772 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6BXL · Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and SAM · the same entry in another collection · chain A against A, TM-score 1.00
- O58832 · AlphaFold monomer V2.0 prediction for 2-(3-amino-3-CARBOXYPROPYL)HISTIDINE synthase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O58832
- Elsewhere: RCSB PDB 6BXL · PDBe 6BXL · UniProt O58832
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