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Lactate dehydrogenase from plasmodium berghei

Analyse Lactate dehydrogenase from plasmodium berghei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1OC4
Type: protein
Length: 630 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-lactate dehydrogenase
EC: 1.1.1.27
UniProt: Q4Z783
Ligands: NAD, OXM
Pockets: 8 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	L-lactate dehydrogenase (EC 1.1.1.27)	protein	315	49% helix, 20% strand	Q4Z783

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
OXM · Oxamic acid · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	391	0.71	0.83	58	GOL
2	234	0.69	0.85	36	NAD, OXM
3	231	0.69	0.85	39	NAD, OXM
4	63	0.58	0.90	22	empty
5	103	0.41	0.76	24	empty

Interfaces

1 interface between chains.

A–B · 1360 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

1OC4 · Lactate dehydrogenase from Plasmodium berghei · 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
Every structure of UniProt Q4Z783
Elsewhere: RCSB PDB 1OC4 · PDBe 1OC4 · UniProt Q4Z783

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