Research workbench
Human JMJD5 in complex with mn, nog and RPS6 (129-144) (complex-1)
Analyse Human JMJD5 in complex with mn, nog and RPS6 (129-144) (complex-1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F4P
- 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
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jmjc domain-containing protein 5 (EC 1.14.11.47) | protein | 236 | 26% helix, 33% strand | Q8N371 |
| B | 40S ribosomal protein S6 | protein | 1 | 0% helix, 0% strand | P62753 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A, B
- MN · Manganese (II) ion · metal · chains A, B
- 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.
Interfaces
1 interface between chains.
- A–B · 215 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6F4P · Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1) · 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 6F4P · PDBe 6F4P · UniProt Q8N371 · UniProt P62753
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