Research workbench
Crystal structure of arabidopsis ARID5 arid-phd cassette in complex with H3K4ME3 peptide and DNA
Analyse Crystal structure of arabidopsis ARID5 arid-phd cassette in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LQF
- Type
- protein + DNA
- Length
- 205 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- At-rich interactive domain-containing protein 4; 15-mer peptide from histone H3.2; DNA…
- UniProt
- Q6NQ79, P59226
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | At-rich interactive domain-containing protein 4 | protein | 175 | 39% helix, 6% strand | Q6NQ79 |
| P | 15-mer peptide from histone H3.2 | protein | 6 | 0% helix, 50% strand | P59226 |
| B, C | DNA (5'-D(*TP*TP*TP*AP*GP*AP*TP*CP*TP*AP*AP*A)-3') | dna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.63 | 0.81 | 22 | empty |
| 2 | 54 | 0.39 | 0.81 | 16 | empty |
| 3 | 103 | 0.35 | 0.74 | 19 | empty |
| 4 | 65 | 0.31 | 0.75 | 12 | empty |
| 5 | 62 | 0.26 | 0.73 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–P · 718 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 514 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–B · 419 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 391 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–B · 14 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 6LQF · Crystal structure of Arabidopsis ARID5 ARID-PHD cassette in complex with H3K4me3 peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NQ79 · AlphaFold monomer V2.0 prediction for at-rich interactive domain- containing protein 4… · a predicted model of the same protein · chain A against A, TM-score 0.87
- P59226 · AlphaFold monomer V2.0 prediction for histone H3.2 (P59226) · a predicted model of the same protein · chain P against A, TM-score 0.53
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 Q6NQ79
- Every structure of UniProt P59226
- Elsewhere: RCSB PDB 6LQF · PDBe 6LQF · UniProt Q6NQ79 · UniProt P59226
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