Structure of PDB 5kah Chain D Binding Site BS01

Receptor Information

>5kah Chain D (length=421) Species: 55952 (Streptomyces toyocaensis)

TDGLWAALTEAAASVEKLLATLPEHGARSSAERAEIAAAHDAARALRVRF
LDTHADAVYDRLTDHRRVHLRLAELVEAAATAFPGLVPTQQQLAVERSLP
QAAKEGHEIDQGIFLRAVLRSPLAGPHLLDAMLRPTPRALELLPEFVRTG
EVEMEAVHLERRDGVARLTMCRDDRLNAEDGQQVDDMETAVDLALLDPGV
RVGLLRGGVMSHPRYRGKRVFSAGINLKYLSQGGISLVDFLMRRELGYIH
KLVRGVLTNDDRPGWWHSPRIEKPWVAAVDGFAIGGGAQLLLVFDRVLAS
SDAYFSLPKEGIIPGAANLRLGRFAGPRVSRQVILEGRRIWAKEPEARLL
VDEVVEPDELDAAIERSLTRLDGDAVLANRRMLNLADESPDGFRAYMAEF
ALMQALRLYGHDTIDKVGRFG

Ligand information

• Ligand ID: YE1
• InChI: InChI=1S/C29H43N8O19P3/c1-29(2,24(43)27(44)33-4-3-19(40)31-5-6-32-20(41)9-15-7-16(38)10-17(39)8-15)12-53-59(50,51)56-58(48,49)52-11-18-23(55-57(45,46)47)22(42)28(54-18)37-14-36-21-25(30)34-13-35-26(21)37/h7-8,10,13-14,18,22-24,28,38-39,42-43H,3-6,9,11-12H2,1-2H3,(H,31,40)(H,32,41)(H,33,44)(H,48,49)(H,50,51)(H2,30,34,35)(H2,45,46,47)/t18-,22-,23-,24+,28-/m1/s1
• InChIKey: MSJGSRHUBFYIJV-CECATXLMSA-N
• SMILES:
  CACTVS 3.341: CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCNC(=O)Cc4cc(O)cc(O)c4
  ACDLabs 10.04: O=C(NCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)Cc4cc(O)cc(O)c4
  OpenEye OEToolkits 1.5.0: CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCNC(=O)Cc4cc(cc(c4)O)O)O
  CACTVS 3.341: CC(C)(CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCNC(=O)Cc4cc(O)cc(O)c4
  OpenEye OEToolkits 1.5.0: CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCNC(=O)Cc4cc(cc(c4)O)O)O
• Formula: C29 H43 N8 O19 P3
• ZINC: ZINC000196255742
• PDB chain: 5kah Chain D Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5kah Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase.
• Resolution: 2.779 Å
• Binding residue (original residue number in PDB): R185 L186 A188 E189 H222 R224 Y225 A233 G234 I235 N236 L237 K238 F250 R254 I294 G295 G296 Q299 I324 G327 F432
• Binding residue (residue number reindexed from 1): R175 L176 A178 E179 H212 R214 Y215 A223 G224 I225 N226 L227 K228 F240 R244 I284 G285 G286 Q289 I312 G315 F420
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): I235 G296 Q299
• Catalytic site (residue number reindexed from 1): I225 G286 Q289
• Enzyme Commision number: 1.13.11.80: (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase.

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
• GO:0042802 identical protein binding

Biological Process

• GO:0006635 fatty acid beta-oxidation
• GO:0017000 antibiotic biosynthetic process

External links

• PDB: RCSB:5kah, PDBe:5kah, PDBj:5kah
• PDBsum: 5kah
• PubMed: 28695857
• UniProt: Q8KLK7|DPGC_STRTO (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase (Gene Name=BU52_01220)