Research workbench
Structure of methylene-tetrahydromethanopterin dehydrogenase from methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT
Analyse Structure of methylene-tetrahydromethanopterin dehydrogenase from methylorubrum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TLK
- Type
- protein
- Length
- 1,729 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional protein mdta
- EC
- 1.5.1.-, 1.5.1.5
- UniProt
- P55818
- Ligands
- NAP, H4M, MG, CL
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional protein mdta (EC 1.5.1.-, 1.5.1.5) | protein | 289 | 43% helix, 20% strand | P55818 |
| B, C, D, E, F | Bifunctional protein mdta (EC 1.5.1.-, 1.5.1.5) | protein | 288 | 43% helix, 20% strand | P55818 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- H4M · 5,10-dimethylene tetrahydromethanopterin · ligand · 2 copies · chains A, C, B
- MG · Magnesium ion · metal
- CL · Chloride ion · ion · chains D, E, F
- FMT · Formic acid · additive · 13 copies · chains A, D, C, B, E, F
- GOL · Glycerol · additive · 6 copies · chains C, A, E, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.79 | 0.83 | 96 | empty |
| 2 | 342 | 0.78 | 0.89 | 41 | CL |
| 3 | 382 | 0.76 | 0.86 | 42 | empty |
| 4 | 543 | 0.64 | 0.75 | 54 | NAP, H4M |
| 5 | 517 | 0.64 | 0.76 | 44 | NAP, GOL |
Interfaces
11 interfaces between chains.
- A–B · 639 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 604 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 586 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 580 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 578 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6TLK · Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum… · the same entry in another collection · chain F against F, 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 6TLK · PDBe 6TLK · UniProt P55818
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.