Research workbench
Crystal structure of MLL1 PHD3-bromo complexed with H3(1-9)K4ME2 peptide
Analyse Crystal structure of MLL1 PHD3-bromo complexed with H3(1-9)K4ME2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LQI
- Type
- protein
- Length
- 556 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MLL1 PHD3-bromo; Histone H3
- UniProt
- Q03164, P68431
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MLL1 PHD3-bromo | protein | 176 | 52% helix, 7% strand | Q03164 |
| B | MLL1 PHD3-bromo | protein | 177 | 50% helix, 7% strand | Q03164 |
| C | MLL1 PHD3-bromo | protein | 181 | 50% helix, 7% strand | Q03164 |
| R | Histone H3 | protein | 6 | 0% helix, 17% strand | P68431 |
| S | Histone H3 | protein | 7 | 0% helix, 14% strand | P68431 |
| T | Histone H3 | protein | 9 | 0% helix, 22% strand | P68431 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.77 | 0.79 | 104 | empty |
| 2 | 81 | 0.74 | 0.97 | 27 | empty |
| 3 | 282 | 0.59 | 0.78 | 41 | empty |
| 4 | 96 | 0.37 | 0.75 | 25 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1601 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 837 Ų buried · 12 hydrogen bonds · protein-protein
- C–T · 583 Ų buried · 10 hydrogen bonds · protein-protein
- A–R · 551 Ų buried · 10 hydrogen bonds · protein-protein
- B–S · 524 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (methylation).
Compared structures
- 3LQI · Crystal structure of MLL1 PHD3-Bromo complexed with H3(1-9)K4me2 peptide · the same entry in another collection · chain A against A, TM-score 1.00
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 Q03164
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 3LQI · PDBe 3LQI · UniProt Q03164 · UniProt P68431
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