Research workbench
Crystal structure of ADCP1 tandem agenet domain 1-2 in complex with H3K9ME1
Analyse Crystal structure of ADCP1 tandem agenet domain 1-2 in complex with H3K9ME1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IE4
- Type
- protein
- Length
- 293 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agenet domain-containing protein; H3K9ME1 peptide
- UniProt
- Q500V5
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agenet domain-containing protein | protein | 137 | 9% helix, 50% strand | Q500V5 |
| B, D | H3K9ME1 peptide | protein | 11 | 0% helix, 9% strand | — |
| C | Agenet domain-containing protein | protein | 134 | 10% helix, 49% strand | Q500V5 |
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 | 593 | 0.66 | 0.76 | 54 | empty |
| 2 | 105 | 0.52 | 0.82 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 793 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 722 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 707 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 6IE4 · Crystal structure of ADCP1 tandem Agenet domain 1-2 in complex with H3K9me1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q500V5 · AlphaFold monomer V2.0 prediction for protein agenet domain (agd)-containing P1 (Q500V5) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q500V5
- Elsewhere: RCSB PDB 6IE4 · PDBe 6IE4 · UniProt Q500V5
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