Research workbench
Crystal structure of nolr from sinorhizobium fredii in complex with oligo aa DNA
Analyse Crystal structure of nolr from sinorhizobium fredii in complex with oligo aa DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ON0
- Type
- protein + DNA
- Length
- 474 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nolr; DNA (5 - D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*TP*GP*TP*TP*AP*A)- 3 )…
- UniProt
- Q83TD2
- Pockets
- 13 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nolr | protein | 97 | 64% helix, 12% strand | Q83TD2 |
| E, G | DNA (5 - D(*TP*AP*TP*TP*AP*GP*AP*GP*AP*AP*CP*CP*CP*TP*GP*AP*TP*GP*TP*TP*AP*A)- 3 ) | dna | 22 | — | — |
| F, H | DNA (5 - D(*TP*AP*AP*TP*CP*TP*CP*TP*TP*GP*GP*GP*AP*CP*TP*AP*CP*AP*AP*TP*TP*A)- 3 ) | dna | 21 | — | — |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.57 | 0.77 | 36 | empty |
| 2 | 323 | 0.56 | 0.76 | 37 | empty |
| 3 | 145 | 0.54 | 0.80 | 14 | empty |
| 4 | 145 | 0.51 | 0.79 | 15 | empty |
| 5 | 158 | 0.51 | 0.78 | 19 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1420 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1401 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 874 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- G–H · 870 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- D–G · 508 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 4ON0 · Crystal Structure of NolR from Sinorhizobium fredii in complex with oligo AA 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 Q83TD2
- Elsewhere: RCSB PDB 4ON0 · PDBe 4ON0 · UniProt Q83TD2
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