MolNFT v1 · #140820 · protein

Crystal structure of pullulanase from klebsiella pneumoniae complex at 10 mm gamma-cyclodextrin

5YNH · Pula protein: “Crystal structure of pullulanase from klebsiella pneumoniae complex at 10 mm gamma-cyclodextrin”. X-ray diffraction, 2 ligands (GLC, CA), 8 pockets (best druggability 0.60). MolNFT v1 #140820 on GenesisL1: 3D…

PDB: 5YNH
Type: protein
Length: 1,055 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pula protein
UniProt: W9BQ28
Ligands: GLC, CA
Pockets: 8 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pula protein	protein	1055	28% helix, 23% strand	W9BQ28

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 16 copies · chains A
CA · Calcium ion · metal · 5 copies · chains A
GOL · Glycerol · additive · chains A

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

Pockets

8 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	233	0.60	0.80	37	empty
2	323	0.59	0.77	41	GLC, GOL
3	160	0.49	0.78	27	empty
4	161	0.45	0.76	24	empty
5	71	0.35	0.76	16	empty

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5YNH · Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM… · 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 W9BQ28
Elsewhere: RCSB PDB 5YNH · PDBe 5YNH · UniProt W9BQ28

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