MolNFT v1 · #59380 · protein

Crystal structure of the apo form of spermidine synthase from trypanosoma cruzi at 2.5 a resolution

3BWB: “Crystal structure of the apo form of spermidine synthase from trypanosoma cruzi at 2.5 a resolution”. X-ray diffraction, 3 pockets (best druggability 0.77). MolNFT v1 #59380 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3BWB
Type: protein
Length: 571 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spermidine synthase
EC: 2.5.1.16
UniProt: Q4DA73
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spermidine synthase (EC 2.5.1.16)	protein	288	30% helix, 29% strand	Q4DA73
B	Spermidine synthase (EC 2.5.1.16)	protein	283	31% helix, 29% strand	Q4DA73

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	494	0.77	0.85	60	empty
2	551	0.76	0.84	63	empty
3	128	0.41	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 1896 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified (engineered).

Compared structures

3BWB · Crystal structure of the apo form of spermidine synthase from Trypanosoma cruzi at 2.5 A… · 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 Q4DA73
Elsewhere: RCSB PDB 3BWB · PDBe 3BWB · UniProt Q4DA73

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