Research workbench

Pectate lyase B from verticillium dahliae

Analyse Pectate lyase B from verticillium dahliae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BBV
Type: protein
Length: 596 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pectate lyase B
UniProt: G2X3Y1
Ligands: MAN, CA
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pectate lyase B	protein	298	10% helix, 44% strand	G2X3Y1

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains B

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

Pockets

2 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	270	0.55	0.77	29	empty
2	244	0.54	0.77	39	empty

Interfaces

1 interface between chains.

A–B · 571 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 glycan (O-glycosylation).

Compared structures

7BBV · Pectate lyase B from Verticillium dahliae · 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 G2X3Y1
Elsewhere: RCSB PDB 7BBV · PDBe 7BBV · UniProt G2X3Y1

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