MolNFT v1 · #148370 · protein

Human JMJD5 in complex with mn and 2OG.

6F4N · Jmjc domain-containing protein 5: “Human JMJD5 in complex with mn and 2OG.”. X-ray diffraction, 2 ligands (AKG, MN), 3 pockets (best druggability 0.45). MolNFT v1 #148370 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6F4N
Type: protein
Length: 484 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Jmjc domain-containing protein 5
EC: 1.14.11.47
UniProt: Q8N371
Ligands: AKG, MN
Pockets: 3 · best druggability 0.45

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	241	26% helix, 33% strand	Q8N371
B	Jmjc domain-containing protein 5 (EC 1.14.11.47)	protein	243	26% helix, 33% strand	Q8N371

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	118	0.45	0.78	21	empty
2	102	0.42	0.78	22	empty
3	59	0.33	0.77	15	empty

Interfaces

1 interface between chains.

A–B · 373 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6F4N · Human JMJD5 in complex with MN and 2OG. · 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 B against A, TM-score 0.98

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
Elsewhere: RCSB PDB 6F4N · PDBe 6F4N · UniProt Q8N371

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