MolNFT v1 · #156492 · protein

Catalytic domain of GH30 xylanase C from talaromyces cellulolyticus

6M5Z: “Catalytic domain of GH30 xylanase C from talaromyces cellulolyticus”. X-ray diffraction, 1 ligand (MAN), 2 pockets (best druggability 0.64). MolNFT v1 #156492 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6M5Z
Type: protein
Length: 866 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GH30 xylanase C
Ligands: MAN
Pockets: 2 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	GH30 xylanase C	protein	433	23% helix, 29% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B
ACT · Acetate ion · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	580	0.64	0.75	76	empty
2	54	0.30	0.75	12	ACT

Interfaces

1 interface between chains.

A–B · 205 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan, 2 modified (disulfide, O-glycosylation, cyclization).

Compared structures

6M5Z · Catalytic domain of GH30 xylanase C from Talaromyces cellulolyticus · 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 6M5Z · PDBe 6M5Z

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