Research workbench
Crystal structure of tmargbp domain 1 in complex with the guanidinium ion
Analyse Crystal structure of tmargbp domain 1 in complex with the guanidinium ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y16
- Type
- protein
- Length
- 254 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amino acid ABC transporter, periplasmic amino acid-binding PROTEIN,AMINO acid ABC…
- UniProt
- Q9WZ62
- Ligands
- GAI
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Amino acid ABC transporter, periplasmic amino acid-binding PROTEIN,AMINO acid ABC transporter, periplasmic amino acid-binding protein | protein | 127 | 36% helix, 23% strand | Q9WZ62 |
Ligands and binding sites
- GAI · Guanidine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.35 | 0.79 | 13 | empty |
| 2 | 101 | 0.35 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 484 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6Y16 · Crystal structure of tmargbp domain 1 in complex with the guanidinium ion · 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 Q9WZ62
- Elsewhere: RCSB PDB 6Y16 · PDBe 6Y16 · UniProt Q9WZ62
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