Research workbench
F factor trai relaxase domain
Analyse F factor 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
- 1P4D
- Type
- protein
- Length
- 827 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trai protein
- EC
- 3.6.1.-
- UniProt
- P14565
- Ligands
- MG
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trai protein (EC 3.6.1.-) | protein | 275 | 40% helix, 22% strand | P14565 |
| B, C | Trai protein (EC 3.6.1.-) | protein | 276 | 40% helix, 21% strand | P14565 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.77 | 0.80 | 77 | EDO |
| 2 | 498 | 0.63 | 0.76 | 52 | empty |
| 3 | 239 | 0.51 | 0.76 | 30 | empty |
| 4 | 194 | 0.49 | 0.76 | 26 | empty |
| 5 | 204 | 0.47 | 0.75 | 37 | MG |
Interfaces
2 interfaces between chains.
- A–B · 956 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 790 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 1P4D · PDBe 1P4D · UniProt P14565
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