Research workbench
Crystal structure of ADP, AMP, and FMN bound TM379
Analyse Crystal structure of ADP, AMP, and FMN bound TM379 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T6Y
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin KINASE/FMN adenylyltransferase
- UniProt
- Q9WZW1
- Ligands
- ADP, AMP, FMN
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin KINASE/FMN adenylyltransferase | protein | 268 | 32% helix, 28% strand | Q9WZW1 |
| B | Riboflavin KINASE/FMN adenylyltransferase | protein | 270 | 33% helix, 25% strand | Q9WZW1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.86 | 0.87 | 83 | AMP |
| 2 | 544 | 0.70 | 0.79 | 42 | AMP |
| 3 | 70 | 0.61 | 0.90 | 18 | empty |
| 4 | 147 | 0.56 | 0.82 | 23 | empty |
| 5 | 114 | 0.51 | 0.81 | 20 | FMN |
Interfaces
1 interface between chains.
- A–B · 893 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1T6Y · Crystal structure of ADP, AMP, and FMN bound TM379 · 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 Q9WZW1
- Elsewhere: RCSB PDB 1T6Y · PDBe 1T6Y · UniProt Q9WZW1
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