MolNFT v1 · #29063 · protein
Crystal structure of the probable aminomethyltransferase from bacillus subtilis
1YX2: “Crystal structure of the probable aminomethyltransferase from bacillus subtilis”. X-ray diffraction, 5 pockets (best druggability 0.70). MolNFT v1 #29063 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YX2
- Type
- protein
- Length
- 720 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminomethyltransferase
- EC
- 2.1.2.10
- UniProt
- P54378
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminomethyltransferase (EC 2.1.2.10) | protein | 358 | 26% helix, 38% strand | P54378 |
| B | Aminomethyltransferase (EC 2.1.2.10) | protein | 362 | 26% helix, 37% strand | P54378 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.70 | 0.80 | 65 | empty |
| 2 | 419 | 0.69 | 0.81 | 54 | empty |
| 3 | 113 | 0.47 | 0.79 | 17 | empty |
| 4 | 82 | 0.40 | 0.78 | 13 | empty |
| 5 | 124 | 0.38 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 1YX2 · Crystal Structure of the Probable Aminomethyltransferase from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P54378 · AlphaFold monomer V2.0 prediction for aminomethyltransferase (P54378) · a predicted model of the same protein · chain B 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 P54378
- Elsewhere: RCSB PDB 1YX2 · PDBe 1YX2 · UniProt P54378
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