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Catalytic domain of dbophma

Analyse Catalytic domain of dbophma in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MJF
Type: protein
Length: 2,221 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dbophm
Ligands: SAH
Pockets: 16 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Dbophm	protein	371	39% helix, 15% strand	—
B, D, F	Dbophm	protein	370	38% helix, 15% strand	—
E	Dbophm	protein	369	38% helix, 15% strand	—

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 5 copies · chains A, B, C, D, F

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1016	0.86	0.87	94	empty
2	1094	0.86	0.87	109	SAH
3	1186	0.85	0.86	109	SAH
4	1141	0.84	0.85	115	SAH
5	1174	0.84	0.84	109	SAH

Interfaces

5 interfaces between chains.

C–D · 6116 Å² buried · 72 hydrogen bonds · protein-protein
E–F · 6063 Å² buried · 72 hydrogen bonds · protein-protein
A–B · 6050 Å² buried · 76 hydrogen bonds · protein-protein
B–F · 380 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 89 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6MJF · Catalytic Domain of dbOphMA · 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 6MJF · PDBe 6MJF

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