Research workbench
The structure of native coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase at 2.2A resolution
Analyse The structure of native coenzyme F420-dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U6I
- Type
- protein
- Length
- 3,384 residues
- Chains
- 12
- 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
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | F420-dependent methylenetetrahydromethanopterin dehydrogenase (EC 1.5.99.9) | protein | 282 | 52% helix, 14% strand | P94951 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.86 | 0.87 | 69 | empty |
| 2 | 930 | 0.86 | 0.87 | 68 | empty |
| 3 | 122 | 0.80 | 0.98 | 27 | empty |
| 4 | 125 | 0.79 | 0.97 | 26 | empty |
| 5 | 102 | 0.78 | 0.99 | 27 | empty |
Interfaces
27 interfaces between chains.
- E–F · 3223 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 3191 Ų buried · 50 hydrogen bonds · protein-protein
- I–J · 3190 Ų buried · 48 hydrogen bonds · protein-protein
- K–L · 3170 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 3141 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 1U6I · The Structure of native coenzyme F420-dependent methylenetetrahydromethanopterin… · the same entry in another collection · chain L against L, 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 P94951
- Elsewhere: RCSB PDB 1U6I · PDBe 1U6I · UniProt P94951
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