MolNFT v1 · #21233 · protein

Structural and functional characterization of a novel archaeal phosphodiesterase

1S3M · Hypothetical protein MJ0936: “Structural and functional characterization of a novel archaeal phosphodiesterase”. X-ray diffraction, 1 ligand (NI), 1 pocket (best druggability 0.41). MolNFT v1 #21233 on GenesisL1: 3D structure…

PDB: 1S3M
Type: protein
Length: 330 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein MJ0936
UniProt: Q58346
Ligands: NI
Pockets: 1 · best druggability 0.41

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hypothetical protein MJ0936	protein	165	25% helix, 33% strand	Q58346

Ligands and binding sites

NI · Nickel (II) ion · metal · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	84	0.41	0.79	22	empty

Interfaces

1 interface between chains.

A–B · 563 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1S3M · Structural and Functional Characterization of a Novel Archaeal Phosphodiesterase · the same entry in another collection · chain A against A, TM-score 1.00
Q58346 · AlphaFold monomer V2.0 prediction for phosphodiesterase MJ0936 (Q58346) · a predicted model of the same protein · chain A 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 Q58346
Elsewhere: RCSB PDB 1S3M · PDBe 1S3M · UniProt Q58346

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