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MT0146, the precorrin-6Y methyltransferase (cbit) homolog from M. thermoautotrophicum, adohcy binary complex
Analyse MT0146, the precorrin-6Y methyltransferase (cbit) homolog from M.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L3I
- Type
- protein
- Length
- 1,116 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Precorrin-6Y METHYLTRANSFERASE/PUTATIVE decarboxylase
- UniProt
- O26249
- Ligands
- SAH
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Precorrin-6Y METHYLTRANSFERASE/PUTATIVE decarboxylase | protein | 186 | 33% helix, 31% strand | O26249 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.69 | 0.79 | 56 | SAH |
| 2 | 525 | 0.68 | 0.78 | 60 | SAH |
| 3 | 531 | 0.67 | 0.78 | 61 | SAH |
| 4 | 438 | 0.67 | 0.79 | 56 | SAH |
| 5 | 281 | 0.59 | 0.78 | 47 | SAH |
Interfaces
8 interfaces between chains.
- E–F · 873 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 845 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 839 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 819 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 807 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified, 6 disulfide (engineered, disulfide).
Compared structures
- 1L3I · MT0146, the precorrin-6Y methyltransferase (cbit) homolog from M. thermoautotrophicum… · the same entry in another collection · chain F against F, TM-score 1.00
- O26249 · AlphaFold monomer V2.0 prediction for probable cobalt-precorrin-6B… · a predicted model of the same protein · chain C 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 O26249
- Elsewhere: RCSB PDB 1L3I · PDBe 1L3I · UniProt O26249
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