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MolNFT v1 · #13689 · protein

Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase (dhbd) complexed with 2',6'-dicl dihydroxybiphenyl (dhb)

1LKD · Biphenyl-2,3-diol 1,2-dioxygenase: “Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase (dhbd) complexed with 2',6'-dicl dihydroxybiphenyl…”. X-ray diffraction, 2 ligands (BP6, FE2), 1 pocket (best druggability 0.60). MolNFT…

PDB
1LKD
Type
protein
Length
287 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Biphenyl-2,3-diol 1,2-dioxygenase
EC
1.13.11.39
UniProt
P47228
Ligands
BP6, FE2
Pockets
1 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 41% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ABiphenyl-2,3-diol 1,2-dioxygenase (EC 1.13.11.39)protein28720% helix, 41% strandP47228

Ligands and binding sites

  • BP6 · 2',6'-dichloro-biphenyl-2,6-diol · ligand · 2 copies · chains A
  • FE2 · Fe (II) ion · metal · 2 copies · chains A
  • P6G · Hexaethylene glycol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12380.600.7929FE2, BP6, P6G

Compared structures

  • 1LKD · Crystal structure of 2,3-dihydroxybiphenyl 1,2-dioxygenase (dhbd) complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
  • P47228 · AlphaFold monomer V2.0 prediction for biphenyl-2,3-diol 1,2-dioxygenase (P47228) · a predicted model of the same protein · chain A against A, TM-score 0.99

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