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Refined crystal structure of dogfish M4 apo-lactate dehydrogenase

Analyse Refined crystal structure of dogfish M4 apo-lactate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LDM
Type: protein
Length: 329 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: M4 lactate dehydrogenase
EC: 1.1.1.27
UniProt: P00341
Ligands: OXM, NAD
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	M4 lactate dehydrogenase (EC 1.1.1.27)	protein	329	45% helix, 17% strand	P00341

Ligands and binding sites

OXM · Oxamic acid · ligand · 2 copies · chains A
NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	240	0.72	0.87	40	NAD, OXM
2	155	0.42	0.74	24	empty

Compared structures

1LDM · Refined crystal structure of dogfish M4 apo-lactate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
P00341 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (P00341) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P00341
Elsewhere: RCSB PDB 1LDM · PDBe 1LDM · UniProt P00341

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