Research workbench
X-ray structure of the methyltransferase subunit a from methanothermus fervidus in complex with cobalamin
Analyse X-ray structure of the methyltransferase subunit a from methanothermus fervidus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LAA
- Type
- protein
- Length
- 480 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetrahydromethanopterin S-methyltransferase subunit a
- EC
- 2.1.1.86
- UniProt
- E3GWY7
- Ligands
- B12
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetrahydromethanopterin S-methyltransferase subunit a (EC 2.1.1.86) | protein | 161 | 30% helix, 17% strand | E3GWY7 |
| B | Tetrahydromethanopterin S-methyltransferase subunit a (EC 2.1.1.86) | protein | 159 | 31% helix, 16% strand | E3GWY7 |
| C | Tetrahydromethanopterin S-methyltransferase subunit a (EC 2.1.1.86) | protein | 160 | 31% helix, 16% strand | E3GWY7 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.64 | 0.88 | 24 | empty |
| 2 | 114 | 0.63 | 0.87 | 21 | empty |
| 3 | 122 | 0.61 | 0.86 | 22 | empty |
Compared structures
- 5LAA · X-ray structure of the methyltransferase subunit a from methanothermus fervidus in… · the same entry in another collection · chain A against A, 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 E3GWY7
- Elsewhere: RCSB PDB 5LAA · PDBe 5LAA · UniProt E3GWY7
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