Research workbench
Crystal structure of the F plasmid trai relaxase domain with the scissile thymidine base
Analyse Crystal structure of the F plasmid trai relaxase domain with the scissile… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q7T
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein trai
- EC
- 3.6.1.-
- UniProt
- P14565
- Ligands
- TMP, MG
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein trai (EC 3.6.1.-) | protein | 267 | 39% helix, 21% strand | P14565 |
| B | Protein trai (EC 3.6.1.-) | protein | 265 | 40% helix, 20% strand | P14565 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.73 | 0.77 | 84 | empty |
| 2 | 67 | 0.50 | 0.85 | 22 | empty |
| 3 | 71 | 0.41 | 0.80 | 17 | empty |
| 4 | 109 | 0.40 | 0.76 | 26 | MG, TMP |
| 5 | 137 | 0.39 | 0.74 | 30 | MG |
Interfaces
1 interface between chains.
- A–B · 919 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2Q7T · Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base · the same entry in another collection · chain A against A, TM-score 1.00
- P14565 · AlphaFold monomer V2.0 prediction for multifunctional conjugation protein trai (P14565) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P14565
- Elsewhere: RCSB PDB 2Q7T · PDBe 2Q7T · UniProt P14565
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