Research workbench
Histone lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine
Analyse Histone lysine demethylase JMJD2A in complex with T11C peptide substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U4S
- Type
- protein
- Length
- 708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A; Histone 3 tail analog (T11C peptide)
- EC
- 1.14.11.-
- UniProt
- O75164, P68431
- Ligands
- 08P, NI, ZN
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 345 | 30% helix, 25% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 349 | 30% helix, 25% strand | O75164 |
| C | Histone 3 tail analog (T11C peptide) | protein | 8 | 0% helix, 13% strand | P68431 |
| D | Histone 3 tail analog (T11C peptide) | protein | 6 | 0% helix, 17% strand | P68431 |
Ligands and binding sites
- 08P · N-(carboxycarbonyl)-D-cysteine · ligand · 2 copies · chains A, C, B, D
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.70 | 0.97 | 20 | NI, 08P |
| 2 | 441 | 0.60 | 0.76 | 53 | empty |
| 3 | 138 | 0.52 | 0.80 | 29 | empty |
| 4 | 70 | 0.52 | 0.85 | 17 | empty |
| 5 | 103 | 0.51 | 0.82 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 709 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 592 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 445 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, methylation).
Compared structures
- 3U4S · Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to… · the same entry in another collection · chain D against D, TM-score 1.00
- O75164 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 4A (O75164) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain D against A, TM-score 0.61
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 O75164
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 3U4S · PDBe 3U4S · UniProt O75164 · UniProt P68431
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