MolNFT v1 · #141799 · protein

LDHA-MA

5ZJF · L-lactate dehydrogenase a chain: “LDHA-MA”. X-ray diffraction, 1 ligand (9G9), 20 pockets (best druggability 0.89). MolNFT v1 #141799 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZJF
Type: protein
Length: 3,972 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-lactate dehydrogenase a chain
EC: 1.1.1.27
UniProt: P00338
Ligands: 9G9
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	331	45% helix, 18% strand	P00338

Ligands and binding sites

9G9 · 5,5'-[(2R,3S)-2,3-dimethylbutane-1,4-diyl]bis(2H-1,3-benzodioxole) · ligand · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1077	0.89	0.91	114	empty
2	755	0.87	0.90	85	9G9
3	642	0.86	0.90	72	empty
4	340	0.83	0.92	42	empty
5	352	0.82	0.92	42	empty

Interfaces

18 interfaces between chains.

G–H · 2908 Å² buried · 30 hydrogen bonds · protein-protein
K–L · 2889 Å² buried · 23 hydrogen bonds · protein-protein
I–J · 2875 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2865 Å² buried · 23 hydrogen bonds · protein-protein
E–F · 2856 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

5ZJF · LDHA-MA · 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
Every structure of UniProt P00338
Elsewhere: RCSB PDB 5ZJF · PDBe 5ZJF · UniProt P00338

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