MolNFT v1 · #135933 · protein

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

5UDS · Lactate racemization operon protein lare: “Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with mgatp”. X-ray diffraction, 3 ligands (ATP, MG, PO4), 20 pockets (best druggability…

PDB: 5UDS
Type: protein
Length: 1,510 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactate racemization operon protein lare
UniProt: F9UST4
Ligands: ATP, MG, PO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 52% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lactate racemization operon protein lare	protein	264	53% helix, 14% strand	F9UST4
B	Lactate racemization operon protein lare	protein	244	51% helix, 16% strand	F9UST4
C	Lactate racemization operon protein lare	protein	250	53% helix, 14% strand	F9UST4
D	Lactate racemization operon protein lare	protein	239	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	50% helix, 14% strand	F9UST4

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 6 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, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.80	0.96	39	empty
2	901	0.76	0.79	86	ATP, MG
3	429	0.69	0.80	43	ATP, MG
4	353	0.67	0.81	37	ATP, MG
5	456	0.66	0.78	51	ATP, MG

Interfaces

13 interfaces between chains.

C–E · 1175 Å² buried · 7 hydrogen bonds · protein-protein
A–F · 1080 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 836 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 735 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 647 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5UDS · 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 5UDS · PDBe 5UDS · UniProt F9UST4

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