MolNFT v1 · #135937 · protein

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

5UDW · Lactate racemization operon protein lare: “Lare, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with nickel”. X-ray diffraction, 3 ligands (NI, SO4, PO4), 20 pockets (best druggability…

PDB: 5UDW
Type: protein
Length: 1,475 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactate racemization operon protein lare
UniProt: F9UST4
Ligands: NI, SO4, PO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 53% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lactate racemization operon protein lare	protein	253	52% helix, 14% strand	F9UST4
B	Lactate racemization operon protein lare	protein	243	52% helix, 15% strand	F9UST4
C	Lactate racemization operon protein lare	protein	250	53% helix, 14% strand	F9UST4
D	Lactate racemization operon protein lare	protein	240	53% helix, 15% strand	F9UST4
E	Lactate racemization operon protein lare	protein	240	53% helix, 15% strand	F9UST4
F	Lactate racemization operon protein lare	protein	249	53% helix, 14% strand	F9UST4

Ligands and binding sites

NI · Nickel (II) ion · metal · 11 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 14 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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	171	0.81	0.96	38	empty
2	732	0.72	0.78	88	SO4
3	726	0.70	0.77	69	SO4
4	438	0.68	0.80	46	SO4
5	400	0.67	0.80	38	SO4

Interfaces

12 interfaces between chains.

A–F · 854 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 839 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 839 Å² buried · 5 hydrogen bonds · protein-protein
D–F · 619 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 561 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5UDW · 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 E 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 5UDW · PDBe 5UDW · UniProt F9UST4

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