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Crystal structure of mgs-M5, a lactate dehydrogenase enzyme from a medee basin deep-sea metagenome library

Analyse Crystal structure of mgs-M5, a lactate dehydrogenase enzyme from a medee basin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Q3N
Type: protein
Length: 314 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mgs-M5
Ligands: NA, CL
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mgs-M5	protein	314	49% helix, 18% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains A
ACT · Acetate ion · additive · 6 copies · chains A
GOL · Glycerol · additive · 5 copies · chains A
PGE · Triethylene glycol · additive · 2 copies · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	372	0.57	0.75	46	CL, ACT
2	271	0.53	0.75	39	empty
3	60	0.34	0.78	14	empty

Compared structures

4Q3N · Crystal structure of MGS-M5, a lactate dehydrogenase enzyme from a Medee basin deep-sea… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 4Q3N · PDBe 4Q3N

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