Research workbench

Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, apo form

Analyse Lare, a sulfur transferase involved in synthesis of the cofactor for lactate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5UDQ
Type: protein
Length: 1,509 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactate racemization operon protein lare
UniProt: F9UST4
Ligands: SO4, PO4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 6 distinct chains · 53% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lactate racemization operon protein lare	protein	263	54% helix, 13% strand	F9UST4
B	Lactate racemization operon protein lare	protein	245	51% helix, 15% strand	F9UST4
C	Lactate racemization operon protein lare	protein	249	53% helix, 14% strand	F9UST4
D	Lactate racemization operon protein lare	protein	240	52% helix, 15% strand	F9UST4
E	Lactate racemization operon protein lare	protein	262	53% helix, 14% strand	F9UST4
F	Lactate racemization operon protein lare	protein	250	53% helix, 14% strand	F9UST4

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, E, F
PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	217	0.82	0.95	44	empty
2	672	0.71	0.78	67	SO4
3	384	0.70	0.82	38	SO4
4	507	0.68	0.78	48	SO4
5	370	0.67	0.80	40	SO4

Interfaces

13 interfaces between chains.

C–E · 1167 Å² buried · 6 hydrogen bonds · protein-protein
A–F · 1086 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 849 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 678 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 611 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5UDQ · LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase… · the same entry in another collection · chain F against F, TM-score 1.00
F9UST4 · AlphaFold monomer V2.0 prediction for pyridinium-3,5-bisthiocarboxylic acid… · a predicted model of the same protein · chain B 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 F9UST4
Elsewhere: RCSB PDB 5UDQ · PDBe 5UDQ · UniProt F9UST4

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