MolNFT v1 · #168734 · protein

Crystal structure of a putative oligosaccharide periplasmic-binding protein from synechococcus sp. MITS9220 in complex with zinc

6WPM · Substrate-binding protein: “Crystal structure of a putative oligosaccharide periplasmic-binding protein from synechococcus sp. MITS9220…”. X-ray diffraction, 2 ligands (ZN, SO4), 5 pockets (best druggability 0.78). MolNFT v1 #168734…

PDB: 6WPM
Type: protein
Length: 401 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Substrate-binding protein
Ligands: ZN, SO4
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Substrate-binding protein	protein	401	51% helix, 15% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A
SO4 · Sulfate ion · ion · 10 copies · chains A
GOL · Glycerol · additive · chains A
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

5 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	941	0.78	0.81	56	ZN, SO4
2	109	0.77	0.96	26	empty
3	180	0.48	0.75	20	empty
4	91	0.35	0.74	15	empty
5	63	0.30	0.74	13	empty

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

6WPM · Crystal structure of a putative oligosaccharide periplasmic-binding protein from… · 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
Elsewhere: RCSB PDB 6WPM · PDBe 6WPM

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