Research workbench
Crystal structure of the plasmid PCU1 trai relaxase domain
Analyse Crystal structure of the plasmid PCU1 trai relaxase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L57
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mobilization protein trai
- EC
- 3.6.1.-
- UniProt
- Q9X4G2
- Ligands
- MN3, PO4
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mobilization protein trai (EC 3.6.1.-) | protein | 223 | 31% helix, 30% strand | Q9X4G2 |
| B | Mobilization protein trai (EC 3.6.1.-) | protein | 203 | 32% helix, 29% strand | Q9X4G2 |
Ligands and binding sites
- MN3 · Manganese (III) ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 26 copies · chains A, B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.46 | 0.76 | 31 | EDO |
| 2 | 103 | 0.43 | 0.78 | 22 | empty |
| 3 | 117 | 0.41 | 0.76 | 17 | EDO |
| 4 | 82 | 0.35 | 0.75 | 16 | EDO |
| 5 | 70 | 0.29 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 800 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3L57 · Crystal Structure of the Plasmid pCU1 TraI Relaxase Domain · 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 Q9X4G2
- Elsewhere: RCSB PDB 3L57 · PDBe 3L57 · UniProt Q9X4G2
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