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Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with manganese

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: 5UDU
Type: protein
Length: 1,516 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactate racemization operon protein lare
UniProt: F9UST4
Ligands: MN, PO4, SO4
Pockets: 16 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 52% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lactate racemization operon protein lare	protein	268	53% 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, 16% strand	F9UST4
D	Lactate racemization operon protein lare	protein	241	52% helix, 15% strand	F9UST4
E	Lactate racemization operon protein lare	protein	263	52% helix, 14% strand	F9UST4
F	Lactate racemization operon protein lare	protein	250	52% helix, 14% strand	F9UST4

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A, B, C, D, E, F
PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate 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

16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	184	0.81	0.96	37	empty
2	581	0.73	0.81	55	SO4
3	737	0.72	0.78	66	SO4
4	832	0.71	0.77	84	SO4
5	630	0.69	0.78	84	SO4

Interfaces

13 interfaces between chains.

C–E · 1166 Å² buried · 8 hydrogen bonds · protein-protein
A–F · 1081 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 845 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 724 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 630 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5UDU · LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in… · 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 5UDU · PDBe 5UDU · UniProt F9UST4

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