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a Novel D-lactate Dehydrogenase from Sporolactobacillus sp

Analyse a Novel D-lactate Dehydrogenase from Sporolactobacillus sp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XKJ
Type: protein
Length: 664 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.148
Source: Sporolactobacillus inulinus CASD
Molecule: D-lactate dehydrogenase
Ligands: NAD
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · resolution 3.148 · 1 distinct chain · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	D-lactate dehydrogenase	protein	332	39% helix, 15% strand	—

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	728	0.73	0.79	68	NAD
2	653	0.65	0.75	53	NAD
3	390	0.63	0.78	50	empty
4	117	0.41	0.76	19	empty
5	76	0.37	0.77	17	empty

Interfaces

1 interface between chains.

A–B · 2808 Å² buried · 49 hydrogen bonds · protein-protein

Compared structures

4XKJ · A novel D-lactate dehydrogenase from sporolactobacillus sp · the same entry in another collection · chain A 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
Elsewhere: RCSB PDB 4XKJ · PDBe 4XKJ

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