Research workbench
Crystal structure of ADCP1 tandem agenet domain 1-2 in complex with H3K9ME2
Analyse Crystal structure of ADCP1 tandem agenet domain 1-2 in complex with H3K9ME2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IE7
- Type
- protein
- Length
- 568 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agenet domain-containing protein; H3K9ME2 peptide
- UniProt
- Q500V5
- Ligands
- NH4
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agenet domain-containing protein | protein | 133 | 10% helix, 51% strand | Q500V5 |
| E, F | H3K9ME2 peptide | protein | 10 | 0% helix, 20% strand | — |
| B | Agenet domain-containing protein | protein | 131 | 7% helix, 50% strand | Q500V5 |
| C | Agenet domain-containing protein | protein | 128 | 5% helix, 52% strand | Q500V5 |
| G, H | H3K9ME2 peptide | protein | 11 | 36% helix, 0% strand | — |
| D | Agenet domain-containing protein | protein | 134 | 7% helix, 50% strand | Q500V5 |
Ligands and binding sites
- NH4 · Ammonium ion · ion · 4 copies · chains A, B, F, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.68 | 0.84 | 26 | empty |
| 2 | 617 | 0.66 | 0.76 | 61 | empty |
| 3 | 576 | 0.64 | 0.75 | 67 | empty |
| 4 | 270 | 0.62 | 0.81 | 32 | empty |
| 5 | 148 | 0.52 | 0.80 | 25 | empty |
Interfaces
10 interfaces between chains.
- C–D · 839 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 772 Ų buried · 23 hydrogen bonds · protein-protein
- D–H · 752 Ų buried · 12 hydrogen bonds · protein-protein
- C–G · 711 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 694 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 6IE7 · Crystal structure of ADCP1 tandem Agenet domain 1-2 in complex with H3K9me2 · the same entry in another collection · chain H against H, 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 B 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 6IE7 · PDBe 6IE7 · UniProt Q500V5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.