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Crystal structure of isopiperitenol dehydrogenase from pseudomonas aeruginosa complexed with NAD

Analyse Crystal structure of isopiperitenol dehydrogenase from pseudomonas aeruginosa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DJS
Type: protein
Length: 964 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sdr family oxidoreductase
UniProt: A0A554HE32
Ligands: NAD
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sdr family oxidoreductase	protein	239	51% helix, 17% strand	A0A554HE32
B	Sdr family oxidoreductase	protein	241	51% helix, 17% strand	A0A554HE32
C	Sdr family oxidoreductase	protein	233	49% helix, 17% strand	A0A554HE32
D	Sdr family oxidoreductase	protein	251	53% helix, 16% strand	A0A554HE32

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	887	0.84	0.86	66	empty
2	231	0.71	0.87	39	NAD
3	268	0.67	0.83	38	NAD
4	237	0.66	0.83	34	NAD
5	282	0.57	0.77	26	empty

Interfaces

6 interfaces between chains.

A–C · 1694 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 1681 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1425 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1399 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 185 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7DJS · Crystal structure of isopiperitenol dehydrogenase from Pseudomonas aeruginosa complexed… · the same entry in another collection · chain C against C, 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 A0A554HE32
Elsewhere: RCSB PDB 7DJS · PDBe 7DJS · UniProt A0A554HE32

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