MolNFT v1 · #117094 · protein
Crystal of selenomethionine substituted amtr from corynebacterium glutamicum
5DY1 · Tetr family transcriptional regulator: “Crystal of selenomethionine substituted amtr from corynebacterium glutamicum”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.65). MolNFT v1 #117094 on GenesisL1: 3D…
- PDB
- 5DY1
- Type
- protein
- Length
- 403 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tetr family transcriptional regulator
- UniProt
- A0A072Z681
- Ligands
- CA
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tetr family transcriptional regulator | protein | 202 | 71% helix, 1% strand | A0A072Z681 |
| B | Tetr family transcriptional regulator | protein | 201 | 69% helix, 1% strand | A0A072Z681 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, 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 | 286 | 0.65 | 0.81 | 37 | empty |
| 2 | 81 | 0.54 | 0.85 | 17 | empty |
| 3 | 249 | 0.49 | 0.74 | 30 | empty |
| 4 | 105 | 0.47 | 0.79 | 22 | empty |
| 5 | 90 | 0.42 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 924 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5DY1 · Crystal of Selenomethionine substituted AmtR from Corynebacterium glutamicum · 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 A0A072Z681
- Elsewhere: RCSB PDB 5DY1 · PDBe 5DY1 · UniProt A0A072Z681
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.