MolNFT v1 · #167199 · protein

Crystal structure of ancestral apicomplexan lactate dehydrogenase with sulfate.

6VDI: “Crystal structure of ancestral apicomplexan lactate dehydrogenase with sulfate.”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.73). MolNFT v1 #167199 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VDI
Type: protein
Length: 626 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactate dehydrogenase
Ligands: SO4
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lactate dehydrogenase	protein	308	51% helix, 20% strand	—
B	Lactate dehydrogenase	protein	318	50% helix, 20% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	552	0.73	0.81	65	SO4
2	414	0.63	0.77	57	SO4
3	325	0.62	0.79	52	empty
4	158	0.52	0.79	23	empty
5	86	0.37	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 2085 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

6VDI · Crystal structure of ancestral apicomplexan lactate dehydrogenase with sulfate. · 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 6VDI · PDBe 6VDI

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