Research workbench
Non-specific protein-DNA interactions in the SSO7D-DNA complex, NMR, 1 structure
Analyse Non-specific protein-DNA interactions in the SSO7D-DNA complex, NMR, 1 structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BBX
- Type
- protein + DNA
- Length
- 150 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)-3'); DNA-binding protein 7D
- UniProt
- P39476
- Pockets
- 3 · best druggability 0.45
Structure
solution nmr · 2 distinct chains · 14% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA (5'-D(*CP*TP*AP*GP*CP*GP*CP*GP*CP*TP*AP*G)-3') | dna | 12 | — | — |
| C, D | DNA-binding protein 7D | protein | 63 | 14% helix, 27% strand | P39476 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.45 | 0.78 | 17 | empty |
| 2 | 116 | 0.42 | 0.77 | 15 | empty |
| 3 | 69 | 0.28 | 0.73 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 597 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- B–C · 386 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–D · 382 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–C · 376 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 373 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 1BBX · Non-specific protein-DNA interactions in the SSO7D-DNA complex, NMR, 1 structure · the same entry in another collection · chain D against D, TM-score 1.00
- P39476 · AlphaFold monomer V2.0 prediction for DNA-binding protein 7D (P39476) · a predicted model of the same protein · chain C against A, TM-score 0.61
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 P39476
- Elsewhere: RCSB PDB 1BBX · PDBe 1BBX · UniProt P39476
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