Research workbench
Wild type gene-regulating protein ARC/DNA complex
Analyse Wild type gene-regulating protein ARC/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BDT
- Type
- protein + DNA
- Length
- 249 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*TP*AP*TP*CP*AP*T)- 3'); DNA…
- UniProt
- P03050
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (5'- D(*TP*AP*TP*AP*GP*TP*AP*GP*AP*GP*TP*GP*CP*TP*TP*CP*TP*AP*TP*CP*AP*T)- 3') | dna | 22 | — | — |
| F | DNA (5'- D(*AP*AP*TP*GP*AP*TP*AP*GP*AP*AP*GP*CP*AP*CP*TP*CP*TP*AP*CP*TP*AP*T)- 3') | dna | 22 | — | — |
| A | Protein (gene-regulating protein arc) | protein | 52 | 56% helix, 10% strand | P03050 |
| B | Protein (gene-regulating protein arc) | protein | 53 | 60% helix, 9% strand | P03050 |
| C, D | Protein (gene-regulating protein arc) | protein | 50 | 52% helix, 10% strand | P03050 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.63 | 0.78 | 35 | empty |
| 2 | 106 | 0.36 | 0.74 | 18 | empty |
| 3 | 83 | 0.33 | 0.74 | 17 | empty |
| 4 | 58 | 0.26 | 0.73 | 15 | empty |
| 5 | 58 | 0.26 | 0.73 | 18 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1819 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1783 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 943 Ų buried · 91 hydrogen bonds · nucleic-nucleic
- E–A · 452 Ų buried · 9 hydrogen bonds · protein-nucleic
- F–C · 428 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 1BDT · Wild type gene-regulating protein ARC/DNA complex · the same entry in another collection · chain E against E, 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 P03050
- Elsewhere: RCSB PDB 1BDT · PDBe 1BDT · UniProt P03050
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