MolNFT v1 · #103292 · protein + DNA
Conjugative relaxase trwc in complex with mutant orit DNA
4PCB: “Conjugative relaxase trwc in complex with mutant orit DNA”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.73). MolNFT v1 #103292 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PCB
- Type
- protein + DNA
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trwc; DNA 5'- D(P*GP*CP*AP*CP*CP*GP*AP*AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*CP*TP*TP*GP - 3')
- UniProt
- Q47673
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Trwc | protein | 280 | 38% helix, 20% strand | Q47673 |
| B, D | DNA 5'- D(P*GP*CP*AP*CP*CP*GP*AP*AP*GP*GP*TP*GP*CP*GP*TP*AP*TP*TP*CP*TP*TP*GP - 3') | dna | 22 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.73 | 0.78 | 79 | empty |
| 2 | 662 | 0.72 | 0.79 | 65 | PO4 |
| 3 | 316 | 0.63 | 0.80 | 37 | empty |
| 4 | 136 | 0.54 | 0.82 | 18 | empty |
| 5 | 214 | 0.52 | 0.77 | 34 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2210 Ų buried · 67 hydrogen bonds · protein-nucleic
- A–B · 2078 Ų buried · 49 hydrogen bonds · protein-nucleic
- A–C · 793 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 19 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 4PCB · Conjugative Relaxase TrwC in complex with mutant OriT Dna · 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 Q47673
- Elsewhere: RCSB PDB 4PCB · PDBe 4PCB · UniProt Q47673
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.