Research workbench
Periplasmic N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein from bacillus halodurans
Analyse Periplasmic N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IX1
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein
- UniProt
- Q9K9G5
- Ligands
- NFM
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein | protein | 301 | 46% helix, 19% strand | Q9K9G5 |
Ligands and binding sites
- NFM · N-[(4-amino-2-methylpyrimidin-5-yl)methyl]formamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.60 | 0.75 | 59 | empty |
| 2 | 158 | 0.56 | 0.81 | 24 | empty |
| 3 | 164 | 0.55 | 0.80 | 26 | empty |
| 4 | 101 | 0.33 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 983 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3IX1 · Periplasmic N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding protein from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9K9G5 · AlphaFold monomer V2.0 prediction for formylaminopyrimidine-binding protein (Q9K9G5) · a predicted model of the same protein · 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 Q9K9G5
- Elsewhere: RCSB PDB 3IX1 · PDBe 3IX1 · UniProt Q9K9G5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.