Research workbench
Human JMJD5 (Q275C) in complex with MN(II), nog and RPS6-A138C (129- 144) (complex-2)
Analyse Human JMJD5 (Q275C) in complex with MN(II), nog and RPS6-A138C (129- 144)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F4Q
- Type
- protein
- Length
- 237 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jmjc domain-containing protein 5; 40S ribosomal protein S6
- EC
- 1.14.11.47
- UniProt
- Q8N371, P62753
- Ligands
- OGA, MN
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jmjc domain-containing protein 5 (EC 1.14.11.47) | protein | 235 | 25% helix, 33% strand | Q8N371 |
| B | 40S ribosomal protein S6 | protein | 2 | 0% helix, 0% strand | P62753 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.54 | 0.84 | 25 | MN, OGA |
Interfaces
1 interface between chains.
- A–B · 223 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6F4Q · Human JMJD5 (Q275C) in complex with Mn(II), NOG and RPS6-A138C (129-144) (complex-2) · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N371 · AlphaFold monomer V2.0 prediction for bifunctional peptidase and arginyl-hydroxylase… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q8N371
- Every structure of UniProt P62753
- Elsewhere: RCSB PDB 6F4Q · PDBe 6F4Q · UniProt Q8N371 · UniProt P62753
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