MolNFT v1 · #50112 · protein

Structure of LMJPDEB1 in complex with ibmx

2R8Q · Class I phosphodiesterase PDEB1: “Structure of LMJPDEB1 in complex with ibmx”. X-ray diffraction, 3 ligands (IBM, ZN, MG), 3 pockets (best druggability 0.73). MolNFT v1 #50112 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2R8Q
Type: protein
Length: 670 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Class I phosphodiesterase PDEB1
EC: 3.1.4.17
UniProt: Q6S996
Ligands: IBM, ZN, MG
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Class I phosphodiesterase PDEB1 (EC 3.1.4.17)	protein	335	71% helix, 0% strand	Q6S996

Ligands and binding sites

IBM · 3-isobutyl-1-methylxanthine · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B
MG · Magnesium 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	507	0.73	0.82	47	IBM, MG
2	856	0.73	0.77	85	empty
3	473	0.72	0.82	45	IBM, MG

Interfaces

1 interface between chains.

A–B · 818 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2R8Q · Structure of LmjPDEB1 in complex with IBMX · the same entry in another collection · chain B against B, 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 Q6S996
Elsewhere: RCSB PDB 2R8Q · PDBe 2R8Q · UniProt Q6S996

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