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Human B lactate dehydrogenase complexed with NAD+ and 4-hydroxy-1,2,5- oxadiazole-3-carboxylic acid

Analyse Human B lactate dehydrogenase complexed with NAD+ and 4-hydroxy-1,2,5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1T2F
Type: protein
Length: 1,328 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-lactate dehydrogenase B chain
EC: 1.1.1.27
UniProt: P07195
Ligands: NAD, OXQ
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	L-lactate dehydrogenase B chain (EC 1.1.1.27)	protein	332	42% helix, 19% strand	P07195

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
OXQ · 4-hydroxy-1,2,5-oxadiazole-3-carboxylic acid · ligand · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	398	0.82	0.90	50	empty
2	354	0.80	0.90	53	empty
3	201	0.73	0.89	33	NAD, OXQ
4	306	0.73	0.86	42	NAD, OXQ
5	118	0.71	0.92	18	empty

Interfaces

6 interfaces between chains.

C–D · 2689 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2615 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 1524 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 1433 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 986 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1T2F · Human B lactate dehydrogenase complexed with NAD+ and… · the same entry in another collection · chain A against A, TM-score 1.00
P07195 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase B chain (P07195) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P07195
Elsewhere: RCSB PDB 1T2F · PDBe 1T2F · UniProt P07195

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