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Crystal structure of lanthanide-dependent methanol dehydrogenase xoxf from methylomicrobium buryatense 5G

Analyse Crystal structure of lanthanide-dependent methanol dehydrogenase xoxf from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DAM
Type: protein
Length: 563 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lanthanide-dependent methanol dehydrogenase xoxf
Ligands: PQQ, LA, NA
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lanthanide-dependent methanol dehydrogenase xoxf	protein	563	8% helix, 39% strand	—

Ligands and binding sites

PQQ · Pyrroloquinoline quinone · ligand · chains A
LA · Lanthanum (III) ion · metal · chains A
NA · Sodium ion · metal · chains A

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

Pockets

4 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	174	0.65	0.85	33	PQQ
2	160	0.46	0.76	22	empty
3	100	0.43	0.78	20	empty
4	84	0.36	0.75	13	empty

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6DAM · Crystal structure of lanthanide-dependent methanol dehydrogenase XoxF from… · 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 6DAM · PDBe 6DAM

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