Research workbench
Structure of JMJD6 complexd with alpha-ketoglutarate and Fab fragment.
Analyse Structure of JMJD6 complexd with alpha-ketoglutarate and Fab fragment. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LDB
- Type
- protein
- Length
- 761 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6; Antibody Fab fragment…
- EC
- 1.14.11.-
- UniProt
- Q6NYC1
- Ligands
- AKG, HG, FE, SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-) | protein | 334 | 38% helix, 21% strand | Q6NYC1 |
| B | Antibody Fab fragment light chain | protein | 217 | 5% helix, 47% strand | — |
| C | Antibody Fab fragment heavy chain | protein | 210 | 3% helix, 49% strand | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- HG · Mercury (II) ion · metal · 2 copies · chains A
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · 19 copies · chains A, C, B
- GOL · Glycerol · additive · 5 copies · chains A, C, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.69 | 0.80 | 44 | AKG, FE |
| 2 | 561 | 0.62 | 0.75 | 59 | empty |
| 3 | 60 | 0.46 | 0.84 | 21 | empty |
| 4 | 104 | 0.39 | 0.76 | 14 | empty |
| 5 | 99 | 0.36 | 0.74 | 26 | SO4 |
Interfaces
3 interfaces between chains.
- B–C · 1997 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 519 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 412 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3LDB · Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment. · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NYC1 · AlphaFold monomer V2.0 prediction for bifunctional arginine demethylase and… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6NYC1
- Elsewhere: RCSB PDB 3LDB · PDBe 3LDB · UniProt Q6NYC1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.