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Crystal structure of COTB2 in complex with alendronate

Analyse Crystal structure of COTB2 in complex with alendronate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6GGJ
Type
protein
Length
579 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Cyclooctat-9-en-7-ol synthase
EC
4.2.3.146
UniProt
C9K1X5
Ligands
AHD, MG
Pockets
5 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ACyclooctat-9-en-7-ol synthase (EC 4.2.3.146)protein28380% helix, 0% strandC9K1X5
BCyclooctat-9-en-7-ol synthase (EC 4.2.3.146)protein29674% helix, 1% strandC9K1X5

Ligands and binding sites

  • AHD · 4-amino-1-hydroxybutane-1,1-diyldiphosphonate · ligand · 2 copies · chains A, B
  • MG · Magnesium ion · metal · 6 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12660.810.9335AHD, MG
22380.800.9336AHD, MG
31690.790.9521empty
42420.680.8432empty
5520.440.8416empty

Interfaces

1 interface between chains.

  • A–B · 1538 Ų buried · 26 hydrogen bonds · protein-protein

Compared structures

  • 6GGJ · Crystal structure of CotB2 in complex with alendronate · the same entry in another collection · chain A against A, TM-score 1.00
  • C9K1X5 · AlphaFold monomer V2.0 prediction for cyclooctat-9-en-7-ol synthase (C9K1X5) · a predicted model of the same protein · chain A against A, TM-score 1.00

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