Research workbench
Structure of methylene-tetrahydromethanopterin dehydrogenase from methylobacterium extorquens AM1
Analyse Structure of methylene-tetrahydromethanopterin dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LU9
- Type
- protein
- Length
- 861 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylene tetrahydromethanopterin dehydrogenase
- EC
- 1.5.1.5
- UniProt
- P55818
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Methylene tetrahydromethanopterin dehydrogenase (EC 1.5.1.5) | protein | 287 | 42% helix, 21% strand | P55818 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.75 | 0.85 | 39 | empty |
| 2 | 544 | 0.64 | 0.76 | 46 | empty |
| 3 | 523 | 0.64 | 0.76 | 47 | empty |
| 4 | 511 | 0.64 | 0.76 | 46 | empty |
| 5 | 51 | 0.23 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 588 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 588 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 580 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1LU9 · Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- P55818 · AlphaFold monomer V2.0 prediction for bifunctional protein mdta (P55818) · 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 P55818
- Elsewhere: RCSB PDB 1LU9 · PDBe 1LU9 · UniProt P55818
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