MolNFT v1 · #13171 · protein
MT0146, the precorrin-6Y methyltransferase (cbit) homolog from M. thermoautotrophicum, C2 spacegroup W/ long cell
1L3B · Precorrin-6Y METHYLTRANSFERASE/PUTATIVE decarboxylase: “MT0146, the precorrin-6Y methyltransferase (cbit) homolog from M. thermoautotrophicum, C2 spacegroup W/ long…”. X-ray diffraction, 20 pockets (best druggability 0.74). MolNFT…
- PDB
- 1L3B
- Type
- protein
- Length
- 1,488 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Precorrin-6Y METHYLTRANSFERASE/PUTATIVE decarboxylase
- UniProt
- O26249
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Precorrin-6Y METHYLTRANSFERASE/PUTATIVE decarboxylase | protein | 186 | 33% helix, 33% strand | O26249 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.74 | 0.98 | 23 | empty |
| 2 | 1073 | 0.72 | 0.76 | 79 | empty |
| 3 | 57 | 0.72 | 0.98 | 24 | empty |
| 4 | 479 | 0.69 | 0.79 | 51 | empty |
| 5 | 456 | 0.67 | 0.79 | 55 | empty |
Interfaces
14 interfaces between chains.
- F–G · 851 Ų buried · 9 hydrogen bonds · protein-protein
- E–H · 840 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 837 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 821 Ų buried · 9 hydrogen bonds · protein-protein
- B–G · 768 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 1L3B · MT0146, the precorrin-6Y methyltransferase (cbit) homolog from M. thermoautotrophicum, C2… · the same entry in another collection · chain H against H, TM-score 1.00
- O26249 · AlphaFold monomer V2.0 prediction for probable cobalt-precorrin-6B… · a predicted model of the same protein · chain H 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 1L3B · PDBe 1L3B · UniProt O26249
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