Research workbench

BP0997, GH138 enzyme targeting pectin rhamnogalacturonan II

Analyse BP0997, GH138 enzyme targeting pectin rhamnogalacturonan II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HZF
Type: protein
Length: 1,708 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BPA0997
Ligands: SER, NA
Pockets: 9 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BPA0997	protein	860	43% helix, 18% strand	—
B	BPA0997	protein	848	44% helix, 18% strand	—

Ligands and binding sites

SER · Serine · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 5 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1032	0.80	0.81	123	empty
2	1151	0.79	0.81	123	empty
3	76	0.73	0.97	29	SER
4	859	0.72	0.77	75	empty
5	52	0.70	0.98	22	SER

Interfaces

1 interface between chains.

A–B · 242 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 44 modified (engineered).

Compared structures

6HZF · BP0997, GH138 enzyme targeting pectin rhamnogalacturonan II · 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 6HZF · PDBe 6HZF

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