Research workbench
Structure of JMJD6 and Fab fragments
Analyse Structure of JMJD6 and Fab fragments in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LD8
- 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
- HG, FE, SO4
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-) | protein | 334 | 40% helix, 21% strand | Q6NYC1 |
| B | Antibody Fab fragment light chain | protein | 217 | 6% helix, 45% strand | — |
| C | Antibody Fab fragment heavy chain | protein | 210 | 4% helix, 44% strand | — |
Ligands and binding sites
- 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.70 | 0.81 | 48 | FE |
| 2 | 524 | 0.60 | 0.74 | 55 | empty |
| 3 | 67 | 0.58 | 0.89 | 25 | SO4 |
| 4 | 155 | 0.45 | 0.76 | 26 | empty |
| 5 | 122 | 0.40 | 0.75 | 20 | GOL |
Interfaces
3 interfaces between chains.
- B–C · 1956 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 530 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 402 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 Q6NYC1
- Elsewhere: RCSB PDB 3LD8 · PDBe 3LD8 · UniProt Q6NYC1
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