MolNFT v1 · #158919 · protein + DNA
Crystal structure of uvrb mutant bound to duplex DNA
6O8H · Uvrabc system protein B: “Crystal structure of uvrb mutant bound to duplex DNA”. X-ray diffraction, 2 ligands (SO4, CL), 8 pockets (best druggability 0.84). MolNFT v1 #158919 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6O8H
- Type
- protein + DNA
- Length
- 597 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uvrabc system protein B; DNA (5'-D(P*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*CP*C)-3'); DNA…
- UniProt
- P56981
- Ligands
- SO4, CL
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uvrabc system protein B | protein | 571 | 43% helix, 18% strand | P56981 |
| B | DNA (5'-D(P*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*CP*C)-3') | dna | 13 | — | — |
| C | DNA (5'-D(P*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)-3') | dna | 13 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.84 | 0.88 | 65 | empty |
| 2 | 248 | 0.69 | 0.85 | 34 | SO4 |
| 3 | 60 | 0.66 | 0.95 | 25 | empty |
| 4 | 151 | 0.59 | 0.84 | 28 | empty |
| 5 | 135 | 0.49 | 0.79 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 625 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 519 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- A–C · 464 Ų buried · 1 hydrogen bond · protein-nucleic
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 P56981
- Elsewhere: RCSB PDB 6O8H · PDBe 6O8H · UniProt P56981
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