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Crystal structure of an N-terminal mutant of the plasmid PCU1 trai relaxase domain
Analyse Crystal structure of an N-terminal mutant of the plasmid PCU1 trai relaxase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L6T
- Type
- protein
- Length
- 429 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
- NI, MG, NA, CL, PO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mobilization protein trai (EC 3.6.1.-) | protein | 226 | 32% helix, 29% strand | Q9X4G2 |
| B | Mobilization protein trai (EC 3.6.1.-) | protein | 203 | 33% helix, 31% strand | Q9X4G2 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 21 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.58 | 0.76 | 47 | EDO |
| 2 | 147 | 0.54 | 0.81 | 24 | PO4, NA |
| 3 | 116 | 0.49 | 0.80 | 23 | EDO |
| 4 | 80 | 0.32 | 0.74 | 21 | CL |
Interfaces
1 interface between chains.
- A–B · 930 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3L6T · Crystal Structure of an N-terminal Mutant 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 3L6T · PDBe 3L6T · UniProt Q9X4G2
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