Research workbench

Structure of TT0471 protein from thermus thermophilus

Analyse Structure of TT0471 protein from thermus thermophilus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2E37
Type: protein
Length: 2,454 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-lactate dehydrogenase
EC: 1.1.1.27
UniProt: Q5SJA1
Ligands: NAD, SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 48% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, H	L-lactate dehydrogenase (EC 1.1.1.27)	protein	308	47% helix, 21% strand	Q5SJA1
B	L-lactate dehydrogenase (EC 1.1.1.27)	protein	304	49% helix, 24% strand	Q5SJA1
C, G	L-lactate dehydrogenase (EC 1.1.1.27)	protein	310	49% helix, 21% strand	Q5SJA1
D	L-lactate dehydrogenase (EC 1.1.1.27)	protein	302	48% helix, 23% strand	Q5SJA1
E	L-lactate dehydrogenase (EC 1.1.1.27)	protein	304	49% helix, 24% strand	Q5SJA1

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, E, G
SO4 · Sulfate ion · ion · 2 copies · chains B, H

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	830	0.83	0.85	108	NAD
2	1142	0.82	0.83	158	NAD
3	941	0.81	0.83	78	empty
4	863	0.80	0.83	73	empty
5	520	0.76	0.83	62	empty

Interfaces

14 interfaces between chains.

E–F · 1855 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1816 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1804 Å² buried · 28 hydrogen bonds · protein-protein
G–H · 1773 Å² buried · 32 hydrogen bonds · protein-protein
C–F · 963 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

2E37 · Structure of TT0471 protein from Thermus thermophilus · the same entry in another collection · chain H against H, TM-score 1.00
Q5SJA1 · AlphaFold monomer V2.0 prediction for L-lactate dehydrogenase (Q5SJA1) · a predicted model of the same protein · chain D 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 Q5SJA1
Elsewhere: RCSB PDB 2E37 · PDBe 2E37 · UniProt Q5SJA1

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