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

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PDB: 5UDR
Type: protein
Length: 1,488 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-utilizing enzyme of the pp-loopsuperfamily
UniProt: A0A0G9FES3
Ligands: NMN, MN
Pockets: 18 · best druggability 0.81

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	257	53% helix, 14% strand	A0A0G9FES3
B	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	243	52% helix, 15% strand	A0A0G9FES3
C	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	247	51% helix, 15% strand	A0A0G9FES3
D	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	232	52% helix, 15% strand	A0A0G9FES3
E	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	260	53% helix, 14% strand	A0A0G9FES3
F	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	249	53% helix, 15% strand	A0A0G9FES3

Ligands and binding sites

NMN · Beta-nicotinamide ribose monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
MN · Manganese (II) ion · metal · 2 copies · chains A, B, C, D, E, F

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

Pockets

18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	166	0.81	0.96	38	empty
2	655	0.69	0.78	68	empty
3	607	0.67	0.77	55	empty
4	471	0.66	0.78	54	empty
5	445	0.64	0.77	44	empty

Interfaces

13 interfaces between chains.

C–E · 1161 Å² buried · 7 hydrogen bonds · protein-protein
A–F · 1044 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 849 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 673 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 630 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5UDR · LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in… · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A0G9FES3
Elsewhere: RCSB PDB 5UDR · PDBe 5UDR · UniProt A0A0G9FES3

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