MolNFT v1 · #44970 · protein
NMR structure of KDM5B PHD1 finger in complex with H3K4ME0(1-10AA)
2MNZ · Lysine-specific demethylase 5B: “NMR structure of KDM5B PHD1 finger in complex with H3K4ME0(1-10AA)”. Solution nmr, 1 ligand (ZN). MolNFT v1 #44970 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2MNZ
- Type
- protein
- Length
- 65 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5B; H3K4ME0
- EC
- 1.14.11.-
- UniProt
- Q9UGL1
- Ligands
- ZN
Structure
solution nmr · 2 distinct chains · 9% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B (EC 1.14.11.-) | protein | 55 | 11% helix, 9% strand | Q9UGL1 |
| B | H3K4ME0 | protein | 10 | 0% helix, 20% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 573 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2MNZ · NMR Structure of KDM5B PHD1 finger in complex with H3K4me0(1-10aa) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UGL1 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5B (Q9UGL1) · a predicted model of the same protein · chain A against A, TM-score 0.72
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 Q9UGL1
- Elsewhere: RCSB PDB 2MNZ · PDBe 2MNZ · UniProt Q9UGL1
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