Research workbench
Mouse gabp ALPHA/BETA domain bound to DNA
Analyse Mouse gabp ALPHA/BETA domain bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AWC
- Type
- protein + DNA
- Length
- 305 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*AP*(BRU) P*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*AP*(CBR)P*AP*CP*(CBR)…
- UniProt
- Q00422, Q00420
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'-D(*AP*AP*(BRU) P*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*AP*(CBR)P*AP*CP*(CBR) P*GP*GP*A)-3') | dna | 21 | — | — |
| E | DNA (5'-D(*TP*TP*CP*CP*GP*GP*(BRU)P*GP*(BRU) P*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*AP*T)-3') | dna | 21 | — | — |
| A | Protein (ga binding protein alpha) | protein | 110 | 51% helix, 11% strand | Q00422 |
| B | Protein (ga binding protein beta 1) | protein | 153 | 54% helix, 0% strand | Q00420 |
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 | 293 | 0.52 | 0.75 | 32 | empty |
| 2 | 112 | 0.46 | 0.79 | 22 | empty |
| 3 | 135 | 0.44 | 0.76 | 15 | empty |
| 4 | 78 | 0.33 | 0.75 | 16 | empty |
| 5 | 72 | 0.27 | 0.72 | 16 | empty |
Interfaces
6 interfaces between chains.
- D–E · 909 Ų buried · 91 hydrogen bonds · nucleic-nucleic
- A–B · 866 Ų buried · 8 hydrogen bonds · protein-protein
- E–A · 451 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–A · 375 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–B · 22 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 modified (nucleotide modification).
Compared structures
- 1AWC · Mouse gabp ALPHA/BETA domain bound to DNA · the same entry in another collection · chain D against D, TM-score 1.00
- Q00422 · AlphaFold monomer V2.0 prediction for ga-binding protein alpha chain (Q00422) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q00420 · AlphaFold monomer V2.0 prediction for ga-binding protein subunit beta-1 (Q00420) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q00422
- Every structure of UniProt Q00420
- Elsewhere: RCSB PDB 1AWC · PDBe 1AWC · UniProt Q00422 · UniProt Q00420
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