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Crystal structure of K. lactis DXO1 (YDR370C) in complex with manganese

Analyse Crystal structure of K. lactis DXO1 (YDR370C) in complex with manganese in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GPU
Type: protein
Length: 331 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: KLLA0E02245P
UniProt: Q6CPU0
Ligands: MN
Pockets: 4 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	KLLA0E02245P	protein	331	34% helix, 29% strand	Q6CPU0

Ligands and binding sites

MN · Manganese (II) ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	342	0.56	0.75	32	MN
2	85	0.33	0.74	15	empty
3	59	0.32	0.76	17	empty
4	62	0.32	0.76	17	empty

Compared structures

4GPU · Crystal structure of K. lactis Dxo1 (YDR370C) in complex with manganese · the same entry in another collection · chain A against A, TM-score 1.00
Q6CPU0 · AlphaFold monomer V2.0 prediction for decapping and exoribonuclease protein 1 (Q6CPU0) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q6CPU0
Elsewhere: RCSB PDB 4GPU · PDBe 4GPU · UniProt Q6CPU0

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