MolNFT v1 · #106710 · protein
Crystal structure of mouse KDM2A-H3K36ME-no complex
4TN7 · Lysine-specific demethylase 2A: “Crystal structure of mouse KDM2A-H3K36ME-no complex”. X-ray diffraction, 2 ligands (FE, NO), 11 pockets (best druggability 0.71). MolNFT v1 #106710 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4TN7
- Type
- protein
- Length
- 814 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 2A; Peptide
- EC
- 1.14.11.27
- UniProt
- P59997
- Ligands
- FE, NO
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lysine-specific demethylase 2A (EC 1.14.11.27) | protein | 329 | 34% helix, 22% strand | P59997 |
| B, D | Lysine-specific demethylase 2A (EC 1.14.11.27) | protein | 68 | 54% helix, 1% strand | P59997 |
| E, F | Peptide | protein | 10 | 0% helix, 10% strand | — |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, E, C
- NO · Nitric oxide · ion · chains A, E
- SIN · Succinic acid · additive · 2 copies · chains A, E, C, F
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 | 252 | 0.71 | 0.86 | 45 | FE, SIN |
| 2 | 290 | 0.70 | 0.84 | 48 | NO, SIN |
| 3 | 651 | 0.68 | 0.77 | 61 | empty |
| 4 | 88 | 0.59 | 0.87 | 22 | empty |
| 5 | 85 | 0.55 | 0.86 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2037 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2033 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 733 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 732 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 246 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
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 P59997
- Elsewhere: RCSB PDB 4TN7 · PDBe 4TN7 · UniProt P59997
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