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Human BMP6 homodimer

Analyse Human BMP6 homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6OMO
Type
protein
Length
208 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Bone morphogenetic protein 6
UniProt
P22004
Ligands
NAG
Pockets
3 · best druggability 0.44

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 45% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
I, JBone morphogenetic protein 6protein10418% helix, 45% strandP22004

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains J, I
  • IPA · Isopropyl alcohol · additive · 6 copies · chains I, J
  • PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains I, J

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1660.440.8114PEG
21430.430.7530empty
3640.270.7321empty

Interfaces

1 interface between chains.

  • I–J · 1219 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

  • 6OMO · Human BMP6 homodimer · the same entry in another collection · chain I against I, TM-score 1.00
  • P22004 · AlphaFold monomer V2.0 prediction for bone morphogenetic protein 6 (P22004) · a predicted model of the same protein · chain I against A, TM-score 0.91

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