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Crystal structure of SPR0440 glycoside hydrolase domain, endo-D from streptococcus pneumoniae R6

Analyse Crystal structure of SPR0440 glycoside hydrolase domain, endo-D from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GDB
Type: protein
Length: 634 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative uncharacterized protein SPR0440
EC: 3.2.1.96
UniProt: Q8CZ52
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative uncharacterized protein SPR0440 (EC 3.2.1.96)	protein	634	20% helix, 36% strand	Q8CZ52

Ligands and binding sites

ACY · Acetic acid · additive · 2 copies · chains A
PGE · Triethylene glycol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	240	0.64	0.82	41	empty
2	165	0.48	0.77	35	empty
3	112	0.43	0.77	17	empty
4	55	0.32	0.77	12	empty
5	77	0.30	0.73	17	empty

Compared structures

3GDB · Crystal structure of Spr0440 glycoside hydrolase domain, Endo-D from Streptococcus… · 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 Q8CZ52
Elsewhere: RCSB PDB 3GDB · PDBe 3GDB · UniProt Q8CZ52

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