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Structure of coenzyme F420 dependent tetrahydromethanopterin reductase from methanobacterium thermoautotrophicum
Analyse Structure of coenzyme F420 dependent tetrahydromethanopterin reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F07
- Type
- protein
- Length
- 1,284 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420-dependent N5,N10- methylenetetrahydromethanopterin reductase
- UniProt
- Q50744
- Ligands
- CL
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Coenzyme F420-dependent N5,N10- methylenetetrahydromethanopterin reductase | protein | 321 | 50% helix, 15% strand | Q50744 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.69 | 0.78 | 57 | MPO, MPD |
| 2 | 594 | 0.69 | 0.78 | 56 | MPO, MPD |
| 3 | 599 | 0.69 | 0.78 | 60 | MPO, MPD |
| 4 | 517 | 0.67 | 0.78 | 55 | MPO, MPD |
| 5 | 434 | 0.63 | 0.77 | 44 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1514 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1503 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 484 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1F07 · Structure of coenzyme F420 dependent tetrahydromethanopterin reductase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q50744 · AlphaFold monomer V2.0 prediction for 5,10-methylenetetrahydromethanopterin reductase… · 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 Q50744
- Elsewhere: RCSB PDB 1F07 · PDBe 1F07 · UniProt Q50744
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