MolNFT v1 · #135557 · protein
Morf double phd finger (dpf) in complex with histone H3K14BU
5U2J: “Morf double phd finger (dpf) in complex with histone H3K14BU”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.62). MolNFT v1 #135557 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5U2J
- Type
- protein
- Length
- 253 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3K14BU; Histone acetyltransferase KAT6B
- EC
- 2.3.1.48
- UniProt
- Q8WYB5
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C | Histone H3K14BU | protein | 16 | 50% helix, 13% strand | — |
| A | Histone acetyltransferase KAT6B (EC 2.3.1.48) | protein | 111 | 16% helix, 9% strand | Q8WYB5 |
| B | Histone acetyltransferase KAT6B (EC 2.3.1.48) | protein | 110 | 13% helix, 11% strand | Q8WYB5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.62 | 0.89 | 22 | empty |
| 2 | 58 | 0.62 | 0.93 | 18 | empty |
| 3 | 56 | 0.59 | 0.90 | 18 | empty |
| 4 | 52 | 0.37 | 0.80 | 14 | empty |
| 5 | 59 | 0.25 | 0.72 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 946 Ų buried · 13 hydrogen bonds · protein-protein
- D–B · 885 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 468 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5U2J · MORF double PHD finger (DPF) in complex with histone H3K14bu · the same entry in another collection · chain D against D, TM-score 1.00
- Q8WYB5 · AlphaFold monomer V2.0 prediction for histone acetyltransferase KAT6B (Q8WYB5) · 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 Q8WYB5
- Elsewhere: RCSB PDB 5U2J · PDBe 5U2J · UniProt Q8WYB5
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