Research workbench
Both zn fingers of GATA1 bound to palindromic DNA recognition site, P21 crystal form
Analyse Both zn fingers of GATA1 bound to palindromic DNA recognition site, P21 crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VD6
- Type
- protein + DNA
- Length
- 136 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*TP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*TP*C)-3'); DNA (5'…
- UniProt
- P17679
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*TP*TP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*TP*C)-3') | dna | 20 | — | — |
| B | DNA (5'- D(*AP*AP*GP*AP*GP*TP*CP*CP*AP*TP*CP*TP*GP*AP*TP*AP*AP*GP*AP*C)-3') | dna | 20 | — | — |
| C | Erythroid transcription factor | protein | 96 | 24% helix, 8% strand | P17679 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.53 | 0.79 | 22 | empty |
| 2 | 105 | 0.51 | 0.82 | 18 | empty |
| 3 | 89 | 0.41 | 0.78 | 17 | empty |
| 4 | 68 | 0.34 | 0.77 | 9 | ACT |
Interfaces
3 interfaces between chains.
- A–C · 991 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 942 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 807 Ų buried · 68 hydrogen bonds · nucleic-nucleic
Compared structures
- 3VD6 · Both Zn Fingers of GATA1 Bound to Palindromic DNA Recognition Site, P21 Crystal Form · the same entry in another collection · chain A against A, TM-score 1.00
- P17679 · AlphaFold monomer V2.0 prediction for erythroid transcription factor (P17679) · a predicted model of the same protein · chain C against A, TM-score 0.60
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 P17679
- Elsewhere: RCSB PDB 3VD6 · PDBe 3VD6 · UniProt P17679
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