MolNFT v1 · #151680 · protein
Hmdii from desulfurobacterium thermolithotrophum reconstituted with fe-guanylylpyridinol (fegp) cofactor and co-crystallized with methenyl-tetrahydrofolate form B
6HUZ · Coenzyme F420-dependent N(5),N(10)…: “Hmdii from desulfurobacterium thermolithotrophum reconstituted with fe-guanylylpyridinol (fegp) cofactor and…”. X-ray diffraction, 3 ligands (FE9, GUE, NA), 4 pockets (best druggability 0.68).…
- PDB
- 6HUZ
- Type
- protein
- Length
- 354 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420-dependent N(5),N(10)- methenyltetrahydromethanopterin reductase-related…
- UniProt
- F0S2B6
- Ligands
- FE9, GUE, NA
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coenzyme F420-dependent N(5),N(10)- methenyltetrahydromethanopterin reductase-related protein | protein | 354 | 56% helix, 11% strand | F0S2B6 |
Ligands and binding sites
- FE9 · iron-guanylyl pyridinol cofactor · ligand · chains A
- GUE · 5,10-Methenyltetrahydrofolate · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.68 | 0.76 | 78 | GOL |
| 2 | 609 | 0.67 | 0.76 | 35 | empty |
| 3 | 332 | 0.59 | 0.77 | 39 | FE9, GUE, GOL |
| 4 | 51 | 0.29 | 0.76 | 11 | empty |
Compared structures
- 6HUZ · HmdII from Desulfurobacterium thermolithotrophum reconstituted with Fe-guanylylpyridinol… · 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 F0S2B6
- Elsewhere: RCSB PDB 6HUZ · PDBe 6HUZ · UniProt F0S2B6
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