Research workbench
Crystal structure of an uncharactertized protein from agrobacterium tumefaciens
Analyse Crystal structure of an uncharactertized protein from agrobacterium tumefaciens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R79
- Type
- protein
- Length
- 449 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A9CHE9
- Ligands
- PLP, PR
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 228 | 50% helix, 15% strand | A9CHE9 |
| B | Uncharacterized protein | protein | 221 | 51% helix, 17% strand | A9CHE9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains B
- PR · Praseodymium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.39 | 0.76 | 23 | PLP |
| 2 | 65 | 0.29 | 0.74 | 14 | empty |
| 3 | 63 | 0.25 | 0.71 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 117 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified, 1 cofactor (engineered, pyridoxal phosphate Schiff base).
Compared structures
- 3R79 · Crystal structure of an uncharactertized protein from Agrobacterium tumefaciens · 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 A9CHE9
- Elsewhere: RCSB PDB 3R79 · PDBe 3R79 · UniProt A9CHE9
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