MolNFT v1 · #82130 · protein + DNA
Both zn fingers of GATA1 bound to palindromic DNA recognition site, P21 crystal form
3VD6 · DNA (5'- D(*TP*TP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*…: “Both zn fingers of GATA1 bound to palindromic DNA recognition site, P21 crystal form”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.53). MolNFT v1…
- 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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