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Crystal structure of aspergillus oryzae RIB2 deaminase in complex with daripp (C-terminal deletion mutant at pH 6.5)

Analyse Crystal structure of aspergillus oryzae RIB2 deaminase in complex with daripp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DS1
Type: protein
Length: 183 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CMP/DCMP-type deaminase domain-containing protein
UniProt: Q2UFA9
Ligands: HJL, ZN
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CMP/DCMP-type deaminase domain-containing protein	protein	183	36% helix, 20% strand	Q2UFA9

Ligands and binding sites

HJL · [(2~{R},3~{S},4~{S})-5-[[2,5-bis(azanyl)-6-oxidanylidene-1~{H}-pyrimidin-4-yl]amino]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate · ligand · chains A
ZN · Zinc ion · metal · 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	137	0.52	0.80	22	HJL

Compared structures

7DS1 · Crystal structure of Aspergillus oryzae Rib2 deaminase in complex with DARIPP (C-terminal… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q2UFA9
Elsewhere: RCSB PDB 7DS1 · PDBe 7DS1 · UniProt Q2UFA9

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