Research workbench
Solution structure of the C-terminal domain of chicken gata-1 bound to DNA, NMR, regularized mean structure
Analyse Solution structure of the C-terminal domain of chicken gata-1 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
- 2GAT
- Type
- protein + DNA
- Length
- 98 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*TP*TP*GP*CP*AP*GP*AP*TP*AP*AP*AP*CP*AP*TP*T)- 3'); DNA…
- UniProt
- P17678
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.72
Structure
solution nmr · 3 distinct chains · 20% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*GP*TP*TP*GP*CP*AP*GP*AP*TP*AP*AP*AP*CP*AP*TP*T)- 3') | dna | 16 | — | — |
| C | DNA (5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*TP*CP*TP*GP*CP*AP*AP*C)- 3') | dna | 16 | — | — |
| A | Erythroid transcription factor gata-1 | protein | 66 | 20% helix, 9% strand | P17678 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.72 | 0.92 | 28 | empty |
| 2 | 267 | 0.64 | 0.82 | 27 | empty |
| 3 | 54 | 0.32 | 0.77 | 13 | empty |
| 4 | 63 | 0.29 | 0.75 | 11 | empty |
| 5 | 58 | 0.27 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 726 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- C–A · 660 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–A · 456 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 2GAT · Solution structure of the C-terminal domain of chicken gata-1 bound to DNA, NMR… · the same entry in another collection · chain B against B, TM-score 1.00
- P17678 · AlphaFold monomer V2.0 prediction for erythroid transcription factor (P17678) · a predicted model of the same protein · chain A against A, TM-score 0.75
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 P17678
- Elsewhere: RCSB PDB 2GAT · PDBe 2GAT · UniProt P17678
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