MolNFT v1 · #125585 · protein

Structure of deubiquitinating enzyme homolog, pyrococcus furiosus JAMM1.

5LD9: “Structure of deubiquitinating enzyme homolog, pyrococcus furiosus JAMM1.”. X-ray diffraction, 2 ligands (ZN, CL), 1 pocket (best druggability 0.75). MolNFT v1 #125585 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LD9
Type: protein
Length: 255 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: JAMM1
UniProt: Q8U1Y4
Ligands: ZN, CL
Pockets: 1 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	JAMM1	protein	129	27% helix, 40% strand	Q8U1Y4
B	JAMM1	protein	126	27% helix, 39% strand	Q8U1Y4

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	599	0.75	0.81	68	CL

Interfaces

1 interface between chains.

A–B · 390 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5LD9 · Structure of deubiquitinating enzyme homolog, Pyrococcus furiosus JAMM1. · the same entry in another collection · chain A against A, TM-score 1.00
Q8U1Y4 · AlphaFold monomer V2.0 prediction for desampylase (Q8U1Y4) · a predicted model of the same protein · chain B 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 Q8U1Y4
Elsewhere: RCSB PDB 5LD9 · PDBe 5LD9 · UniProt Q8U1Y4

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