MolNFT v1 · #143539 · protein

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

6B2M · ATP-utilizing enzyme of the pp-loopsuperfamily: “Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with…”. X-ray diffraction, 2 ligands (COA, PO4), 17 pockets (best druggability 0.81).…

PDB: 6B2M
Type: protein
Length: 1,525 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: COA, PO4
Pockets: 17 · best druggability 0.81

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	268	54% 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	255	51% helix, 14% strand	A0A0G9FES3
D	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	240	53% helix, 15% strand	A0A0G9FES3
E	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	263	53% helix, 15% strand	A0A0G9FES3
F	ATP-utilizing enzyme of the pp-loopsuperfamily	protein	252	53% helix, 14% strand	A0A0G9FES3

Ligands and binding sites

COA · Coenzyme A · ligand · 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

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	174	0.81	0.96	44	empty
2	606	0.71	0.79	65	COA, PO4
3	715	0.70	0.77	66	COA, PO4
4	747	0.70	0.77	74	COA
5	587	0.70	0.78	62	COA, PO4

Interfaces

13 interfaces between chains.

C–E · 1237 Å² buried · 8 hydrogen bonds · protein-protein
A–F · 1193 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 848 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 723 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 641 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6B2M · 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 6B2M · PDBe 6B2M · UniProt A0A0G9FES3

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