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Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (mtd) from methanopyrus kandleri: a methanogenic enzyme with an unusual quarternary structure
Analyse Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (mtd)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QV9
- Type
- protein
- Length
- 846 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- F420-dependent methylenetetrahydromethanopterin dehydrogenase
- EC
- 1.5.99.9
- UniProt
- P94951
- Ligands
- MG
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | F420-dependent methylenetetrahydromethanopterin dehydrogenase (EC 1.5.99.9) | protein | 282 | 53% helix, 13% strand | P94951 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.58 | 0.78 | 20 | empty |
| 2 | 192 | 0.48 | 0.75 | 29 | empty |
| 3 | 176 | 0.48 | 0.76 | 27 | empty |
| 4 | 183 | 0.47 | 0.76 | 19 | empty |
| 5 | 182 | 0.47 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 366 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 363 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 357 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 1QV9 · Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from… · the same entry in another collection · chain A against A, TM-score 1.00
- P94951 · AlphaFold monomer V2.0 prediction for F420-dependent methylenetetrahydromethanopterin… · 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 P94951
- Elsewhere: RCSB PDB 1QV9 · PDBe 1QV9 · UniProt P94951
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