Research workbench
Crystal structure of candidatus methanoperedens nitroreducens DPH2 with 4FE-4S cluster and SAM
Analyse Crystal structure of candidatus methanoperedens nitroreducens DPH2 with 4FE-4S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BXN
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphthamide biosynthesis enzyme DPH2
- UniProt
- A0A062UZ78
- Ligands
- SF4, SAM
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diphthamide biosynthesis enzyme DPH2 | protein | 294 | 36% helix, 20% strand | A0A062UZ78 |
| B | Diphthamide biosynthesis enzyme DPH2 | protein | 316 | 38% helix, 22% strand | A0A062UZ78 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.67 | 0.78 | 59 | SF4, SAM |
| 2 | 208 | 0.66 | 0.85 | 31 | empty |
| 3 | 355 | 0.65 | 0.79 | 44 | SF4, SAM |
| 4 | 77 | 0.36 | 0.76 | 21 | empty |
| 5 | 56 | 0.32 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1632 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6BXN · Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster… · 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 A0A062UZ78
- Elsewhere: RCSB PDB 6BXN · PDBe 6BXN · UniProt A0A062UZ78
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