MolNFT v1 · #158918 · protein + DNA
Crystal structure of uvrb bound to fully duplex DNA
6O8G · Uvrabc system protein B: “Crystal structure of uvrb bound to fully duplex DNA”. X-ray diffraction, 3 ligands (ADP, NA, CL), 20 pockets (best druggability 0.83). MolNFT v1 #158918 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6O8G
- Type
- protein + DNA
- Length
- 1,784 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uvrabc system protein B; DNA (5'-D(*TP*CP*TP*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*C)- 3')…
- UniProt
- P56981
- Ligands
- ADP, NA, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uvrabc system protein B | protein | 564 | 43% helix, 19% strand | P56981 |
| B | Uvrabc system protein B | protein | 568 | 43% helix, 19% strand | P56981 |
| C | Uvrabc system protein B | protein | 560 | 44% helix, 19% strand | P56981 |
| D, F, H | DNA (5'-D(*TP*CP*TP*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*C)- 3') | dna | 15 | — | — |
| E, I | DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)- 3') | dna | 16 | — | — |
| G | DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)- 3') | dna | 15 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · chains E
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.83 | 0.84 | 113 | CL |
| 2 | 1034 | 0.83 | 0.84 | 109 | empty |
| 3 | 1053 | 0.80 | 0.82 | 71 | empty |
| 4 | 423 | 0.78 | 0.87 | 50 | empty |
| 5 | 925 | 0.78 | 0.81 | 65 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1083 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 976 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–H · 940 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–F · 883 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–E · 762 Ų buried · 6 hydrogen bonds · 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 6O8G · PDBe 6O8G · UniProt P56981
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