Research workbench
PHD6 domain of MLL3 in complex with histone H4
Analyse PHD6 domain of MLL3 in complex with histone H4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MLC
- Type
- protein
- Length
- 350 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase 2C; Histone H4
- EC
- 2.1.1.43
- UniProt
- Q8NEZ4, P62805
- Ligands
- ZN, UNX
- Pockets
- 7 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Histone-lysine N-methyltransferase 2C (EC 2.1.1.43) | protein | 84 | 20% helix, 18% strand | Q8NEZ4 |
| B, C | Histone-lysine N-methyltransferase 2C (EC 2.1.1.43) | protein | 85 | 21% helix, 16% strand | Q8NEZ4 |
| E, F | Histone H4 | protein | 6 | 0% helix, 50% strand | P62805 |
Ligands and binding sites
- ZN · Zinc ion · metal · 14 copies · chains A, B, C, D
- UNX · Unknown atom or ion · ion · 7 copies · chains A, B, E, C, D, F
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.50 | 0.77 | 25 | empty |
| 2 | 134 | 0.45 | 0.77 | 28 | UNX |
| 3 | 135 | 0.44 | 0.76 | 25 | GOL |
| 4 | 80 | 0.37 | 0.76 | 18 | UNX |
| 5 | 72 | 0.34 | 0.75 | 18 | GOL |
Interfaces
6 interfaces between chains.
- C–D · 1114 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1109 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 521 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 495 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 326 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6MLC · PHD6 domain of MLL3 in complex with histone H4 · 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 Q8NEZ4
- Every structure of UniProt P62805
- Elsewhere: RCSB PDB 6MLC · PDBe 6MLC · UniProt Q8NEZ4 · UniProt P62805
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