MolNFT v1 · #4470 · protein

Crystal structure of the complex between rhodanese and lipoate

1DP2: “Crystal structure of the complex between rhodanese and lipoate”. X-ray diffraction, 1 ligand (LPB), 3 pockets (best druggability 0.50). MolNFT v1 #4470 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1DP2
Type: protein
Length: 293 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodanese
EC: 2.8.1.1
UniProt: P00586
Ligands: LPB
Pockets: 3 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rhodanese (EC 2.8.1.1)	protein	293	33% helix, 16% strand	P00586

Ligands and binding sites

LPB · 5-[(3S)-1,2-dithiolan-3-yl]pentanoic acid · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	159	0.50	0.78	23	LPB
2	65	0.32	0.75	19	empty
3	67	0.28	0.73	15	empty

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

1DP2 · Crystal structure of the complex between rhodanese and lipoate · the same entry in another collection · chain A against A, TM-score 1.00
P00586 · AlphaFold monomer V2.0 prediction for thiosulfate sulfurtransferase (P00586) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P00586
Elsewhere: RCSB PDB 1DP2 · PDBe 1DP2 · UniProt P00586

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