MolNFT v1 · #17399 · protein + DNA
Conjugative relaxase trwc in complex with orit DNA. metal-free structure.
1OSB · DNA oligonucleotide: “Conjugative relaxase trwc in complex with orit DNA. metal-free structure.”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.69). MolNFT v1 #17399 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1OSB
- Type
- protein + DNA
- Length
- 619 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA oligonucleotide; Trwc protein
- UniProt
- Q47673
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | DNA oligonucleotide | dna | 25 | — | — |
| A | Trwc protein | protein | 287 | 40% helix, 21% strand | Q47673 |
| C | Trwc protein | protein | 282 | 40% helix, 22% strand | Q47673 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.69 | 0.78 | 64 | SO4 |
| 2 | 521 | 0.66 | 0.77 | 57 | SO4 |
| 3 | 426 | 0.61 | 0.77 | 38 | empty |
| 4 | 95 | 0.55 | 0.85 | 17 | SO4 |
| 5 | 94 | 0.51 | 0.83 | 16 | empty |
Interfaces
3 interfaces between chains.
- D–C · 2448 Ų buried · 71 hydrogen bonds · protein-nucleic
- B–A · 2395 Ų buried · 77 hydrogen bonds · protein-nucleic
- A–C · 137 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1OSB · Conjugative Relaxase TrwC in complex with OriT Dna. Metal-free structure. · the same entry in another collection · chain B against B, 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 1OSB · PDBe 1OSB · UniProt Q47673
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