Research workbench
Damage detection by the uvrabc pathway: crystal structure of uvrb bound to fluorescein-adducted DNA
Analyse Damage detection by the uvrabc pathway: crystal structure of uvrb bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NMV
- Type
- protein + DNA
- Length
- 662 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*TP*TP*TP*TP*T)-3'; Uvrabc system protein B
- EC
- 3.1.-.-
- UniProt
- P37954
- Ligands
- ADP, NML, FLU
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(P*TP*TP*TP*TP*T)-3' | dna | 4 | — | — |
| A | Uvrabc system protein B (EC 3.1.-.-) | protein | 620 | 45% helix, 19% strand | P37954 |
| B | Uvrabc system protein B (EC 3.1.-.-) | protein | 38 | 87% helix, 0% strand | P37954 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- NML · N-methylacetamide · ligand · chains D, A
- FLU · 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-benzoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.73 | 0.78 | 84 | ADP |
| 2 | 631 | 0.73 | 0.80 | 68 | empty |
| 3 | 422 | 0.62 | 0.77 | 46 | empty |
| 4 | 196 | 0.51 | 0.76 | 24 | empty |
Interfaces
2 interfaces between chains.
- D–A · 628 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 517 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2NMV · Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to… · the same entry in another collection · chain D against D, TM-score 1.00
- P37954 · AlphaFold monomer V2.0 prediction for uvrabc system protein B (P37954) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P37954
- Elsewhere: RCSB PDB 2NMV · PDBe 2NMV · UniProt P37954
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