MolNFT v1 · #118107 · protein

Co-crystal structure of ldh liganded with oxamate

5ES3 · L-lactate dehydrogenase a chain: “Co-crystal structure of ldh liganded with oxamate”. X-ray diffraction, 1 ligand (OXM), 20 pockets (best druggability 0.89). MolNFT v1 #118107 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5ES3
Type: protein
Length: 2,625 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-lactate dehydrogenase a chain
EC: 1.1.1.27
UniProt: P04642
Ligands: OXM
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 4 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	328	44% helix, 19% strand	P04642
C	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	331	45% helix, 18% strand	P04642
E	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	330	45% helix, 19% strand	P04642
F, D, H, B	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	327	44% helix, 19% strand	P04642

Ligands and binding sites

OXM · Oxamic acid · ligand · 8 copies · chains A, C, E, F, D, H, B, G

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	1063	0.89	0.91	124	empty
2	1001	0.89	0.91	119	empty
3	431	0.69	0.81	42	OXM
4	63	0.68	0.96	17	empty
5	64	0.68	0.95	14	empty

Interfaces

13 interfaces between chains.

C–B · 2692 Å² buried · 25 hydrogen bonds · protein-protein
E–H · 2683 Å² buried · 22 hydrogen bonds · protein-protein
F–G · 2625 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 2618 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1788 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

5ES3 · Co-crystal structure of LDH liganded with oxamate · the same entry in another collection · chain G against G, TM-score 1.00
P04642 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase a chain (P04642) · a predicted model of the same protein · chain F 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 P04642
Elsewhere: RCSB PDB 5ES3 · PDBe 5ES3 · UniProt P04642

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.