MolNFT v1 · #125466 · protein

Oceanobacillus iheyensis macrodomain with ADP

5L9Q · Macrod-type macrodomain: “Oceanobacillus iheyensis macrodomain with ADP”. X-ray diffraction, 2 ligands (ADP, SO4), 2 pockets (best druggability 0.57). MolNFT v1 #125466 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L9Q
Type: protein
Length: 379 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Macrod-type macrodomain
UniProt: Q8EP31
Ligands: ADP, SO4
Pockets: 2 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Macrod-type macrodomain	protein	190	41% helix, 20% strand	Q8EP31
B	Macrod-type macrodomain	protein	189	41% helix, 20% strand	Q8EP31

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	155	0.57	0.82	28	ADP
2	179	0.54	0.79	27	ADP

Interfaces

1 interface between chains.

A–B · 500 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5L9Q · Oceanobacillus iheyensis macrodomain with ADP · the same entry in another collection · 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 Q8EP31
Elsewhere: RCSB PDB 5L9Q · PDBe 5L9Q · UniProt Q8EP31

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