MolNFT v1 · #34028 · protein

Crystal structure of 2-deoxy-scyllo-inosose synthase

2D2X: “Crystal structure of 2-deoxy-scyllo-inosose synthase”. X-ray diffraction, 2 ligands (CO, SO3), 4 pockets (best druggability 0.75). MolNFT v1 #34028 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2D2X
Type: protein
Length: 705 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-deoxy-scyllo-inosose synthase
EC: 4.2.3.-
UniProt: Q9S5E2
Ligands: CO, SO3
Pockets: 4 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-deoxy-scyllo-inosose synthase (EC 4.2.3.-)	protein	353	46% helix, 22% strand	Q9S5E2
B	2-deoxy-scyllo-inosose synthase (EC 4.2.3.-)	protein	352	45% helix, 22% strand	Q9S5E2

Ligands and binding sites

CO · Cobalt (II) ion · metal · 4 copies · chains A, B
SO3 · Sulfite ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1060	0.75	0.77	76	GOL
2	1007	0.73	0.77	73	CO, GOL
3	442	0.63	0.76	46	empty
4	72	0.38	0.78	19	empty

Interfaces

1 interface between chains.

A–B · 1100 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2D2X · Crystal structure of 2-deoxy-scyllo-inosose synthase · the same entry in another collection · chain A against A, TM-score 1.00
Q9S5E2 · AlphaFold monomer V2.0 prediction for 2-deoxy-scyllo-inosose synthase (Q9S5E2) · a predicted model of the same protein · chain B 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 Q9S5E2
Elsewhere: RCSB PDB 2D2X · PDBe 2D2X · UniProt Q9S5E2

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