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Crystal structure of yeast YNU0, YNL200C

Analyse Crystal structure of yeast YNU0, YNL200C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JZT
Type: protein
Length: 486 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical 27.5 kda protein in SPX19-GCR2 intergenic region
UniProt: P40165
Ligands: CL
Pockets: 8 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hypothetical 27.5 kda protein in SPX19-GCR2 intergenic region	protein	243	36% helix, 16% strand	P40165

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

8 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	61	0.66	0.94	20	empty
2	148	0.60	0.84	31	CL
3	90	0.44	0.79	26	empty
4	112	0.43	0.77	19	empty
5	91	0.40	0.77	25	empty

Interfaces

1 interface between chains.

A–B · 1494 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

1JZT · Crystal structure of yeast ynu0, YNL200c · the same entry in another collection · chain A against A, TM-score 1.00
P40165 · AlphaFold monomer V2.0 prediction for NAD(P)H-hydrate epimerase (P40165) · 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 P40165
Elsewhere: RCSB PDB 1JZT · PDBe 1JZT · UniProt P40165

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