MolNFT v1 · #21532 · protein

X-ray structure of YDDE_ECOLI northeast structural genomics consortium target ET25.

1SDJ · Hypothetical protein ydde: “X-ray structure of YDDE_ECOLI northeast structural genomics consortium target ET25.”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.59). MolNFT v1 #21532 on GenesisL1: 3D structure…

PDB: 1SDJ
Type: protein
Length: 310 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein ydde
UniProt: P37757
Ligands: SO4
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein ydde	protein	310	23% helix, 38% strand	P37757

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	213	0.59	0.81	26	SO4
2	65	0.56	0.88	18	empty
3	104	0.43	0.77	18	empty

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

1SDJ · X-ray structure of YDDE_ECOLI northeast structural genomics consortium target ET25. · the same entry in another collection · chain A against A, TM-score 1.00
P37757 · AlphaFold monomer V2.0 prediction for uncharacterized isomerase ydde (P37757) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P37757
Elsewhere: RCSB PDB 1SDJ · PDBe 1SDJ · UniProt P37757

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