Research workbench
Structure of methylene-tetrahydromethanopterin dehydrogenase from methylorubrum extorquens AM1 in a close 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
- 6TM3
- Type
- protein
- Length
- 289 residues
- Chains
- 1
- 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, LI
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 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 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- H4M · 5,10-dimethylene tetrahydromethanopterin · ligand · chains A
- LI · Lithium ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 14 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.57 | 0.76 | 36 | NAP, H4M |
Compared structures
- 6TM3 · Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum… · 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 0.95
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 6TM3 · PDBe 6TM3 · UniProt P55818
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