MolNFT v1 · #147313 · protein + DNA
Crystal structure of ZBTB38 C-terminal zinc fingers 6-9 in complex with methylated DNA
6E93 · Zinc finger and btb domain-containing protein 38: “Crystal structure of ZBTB38 C-terminal zinc fingers 6-9 in complex with methylated DNA”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.72). MolNFT v1 #147313 on…
- PDB
- 6E93
- Type
- protein + DNA
- Length
- 148 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc finger and btb domain-containing protein 38; DNA…
- UniProt
- Q8NAP3
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc finger and btb domain-containing protein 38 | protein | 112 | 44% helix, 14% strand | Q8NAP3 |
| C | DNA (5'-D(*GP*TP*CP*TP*GP*(DCM)P*GP*CP*(DCM) P*GP*AP*TP*GP*AP*GP*TP*GP*C)-3') | dna | 18 | — | — |
| D | DNA (5'-D(*GP*CP*AP*CP*TP*CP*AP*TP*(DCM)P*GP*GP*(DCM) P*GP*CP*AP*GP*AP*C)-3') | dna | 18 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.72 | 0.85 | 43 | empty |
| 2 | 115 | 0.58 | 0.85 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1077 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–D · 826 Ų buried · 76 hydrogen bonds · nucleic-nucleic
- A–D · 568 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6E93 · Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 in complex with methylated DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NAP3 · AlphaFold monomer V2.0 prediction for zinc finger and btb domain- containing protein 38… · a predicted model of the same protein · chain A against A, TM-score 0.86
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 Q8NAP3
- Elsewhere: RCSB PDB 6E93 · PDBe 6E93 · UniProt Q8NAP3
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