MolNFT v1 · #82513 · protein

L-lactate dehydrogenase from thermus caldophilus GK24

3VPG: “L-lactate dehydrogenase from thermus caldophilus GK24”. X-ray diffraction, 10 pockets (best druggability 0.82). MolNFT v1 #82513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3VPG
Type: protein
Length: 1,240 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-lactate dehydrogenase
EC: 1.1.1.27
UniProt: P06150
Pockets: 10 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	L-lactate dehydrogenase (EC 1.1.1.27)	protein	310	49% helix, 21% strand	P06150

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains D

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1008	0.82	0.83	82	empty
2	1107	0.82	0.83	82	empty
3	587	0.69	0.78	56	empty
4	456	0.66	0.78	55	empty
5	476	0.65	0.78	67	GOL

Interfaces

5 interfaces between chains.

B–C · 1816 Å² buried · 30 hydrogen bonds · protein-protein
A–D · 1815 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 797 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 793 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 59 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3VPG · L-lactate dehydrogenase from Thermus caldophilus GK24 · the same entry in another collection · chain A against A, TM-score 1.00
P06150 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (P06150) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P06150
Elsewhere: RCSB PDB 3VPG · PDBe 3VPG · UniProt P06150

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