Research workbench

Ydhf, an aldo-keto reductase from E.COLI complexed with NADPH

Analyse Ydhf, an aldo-keto reductase from E.COLI complexed with NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1OG6
Type: protein
Length: 889 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical oxidoreductase ydhf
UniProt: P76187
Ligands: NAP
Pockets: 10 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical oxidoreductase ydhf	protein	297	45% helix, 16% strand	P76187
B	Hypothetical oxidoreductase ydhf	protein	294	41% helix, 15% strand	P76187
C	Hypothetical oxidoreductase ydhf	protein	298	44% helix, 16% strand	P76187

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	388	0.66	0.80	40	NAP
2	313	0.65	0.81	44	NAP
3	295	0.64	0.81	47	NAP
4	173	0.55	0.80	34	empty
5	190	0.51	0.77	30	empty

Interfaces

3 interfaces between chains.

B–C · 1061 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 1005 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 971 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1OG6 · ydhF, an aldo-keto reductase from E.coli complexed with NADPH · the same entry in another collection · chain A against A, TM-score 1.00
P76187 · AlphaFold monomer V2.0 prediction for oxidoreductase ydhf (P76187) · a predicted model of the same protein · chain C 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 P76187
Elsewhere: RCSB PDB 1OG6 · PDBe 1OG6 · UniProt P76187

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