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Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, C176A variant

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: 6B2O
Type: protein
Length: 1,500 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: PO4, SO4
Pockets: 17 · best druggability 0.82

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	261	52% helix, 13% strand	A0A0G9FES3
B	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	247	51% helix, 15% strand	A0A0G9FES3
C	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	249	53% helix, 15% strand	A0A0G9FES3
D	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	233	53% helix, 15% strand	A0A0G9FES3
E	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	261	53% helix, 15% strand	A0A0G9FES3
F	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	249	51% helix, 14% strand	A0A0G9FES3

Ligands and binding sites

PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, E, F

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

Pockets

17 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	235	0.82	0.94	45	empty
2	804	0.72	0.78	79	PO4, SO4
3	453	0.72	0.82	45	SO4
4	731	0.72	0.78	70	SO4
5	446	0.68	0.80	70	empty

Interfaces

13 interfaces between chains.

C–E · 1169 Å² buried · 8 hydrogen bonds · protein-protein
A–F · 1060 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 839 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 636 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 619 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6B2O · LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase… · 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 6B2O · PDBe 6B2O · UniProt A0A0G9FES3

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