Structure of PDB 1jdb Chain K Binding Site BS09

Receptor Information

>1jdb Chain K (length=1060) Species: 562 (Escherichia coli)

MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSN
PATIMTDPEMADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCAL
ELERQGVLEEFGVTMIGATADAIDKAEDRRRFDVAMKKIGLETARSGIAH
TMEEALAVAADVGFPCIIRPSFTMGGSGGGIAYNREEFEEICARGLDLSP
TKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGDSITV
APAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM
NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEP
SIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALR
GLEVGATGFDPKVSLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVD
GVFNLTNIDRWFLVQIEELVRLEEKVAEVGITGLNADFLRQLKRKGFADA
RLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEE
CEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN
CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKL
ARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEM
AVEKAKEIGYPLVVRPAMEIVYDEADLRRYFQTAAPVLLDHFLDDAVEVD
VDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQV
QKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAK
VAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRS
TGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAK
LLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYI
INTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVI
SVQEMHAQIK

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 1jdb Chain K Residue 1096

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1jdb The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): R714 F754 L755 E760 A784 G785 H787 E840
• Binding residue (residue number reindexed from 1): R715 F742 L743 E748 A772 G773 H775 E828
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): R128 R168 K201 E214 H242 N282 Q284 E298 N300 R302 D337 G506 K633 R714 E760 D768 Q828 E840 N842 R847 P900
• Catalytic site (residue number reindexed from 1): R129 R169 K202 E215 H243 N283 Q285 E299 N301 R303 D338 G507 K634 R715 E748 D756 Q816 E828 N830 R835 P888
• Enzyme Commision number: 6.3.4.16: carbamoyl-phosphate synthase (ammonia).
  6.3.5.5: carbamoyl-phosphate synthase (glutamine-hydrolyzing).

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004087 carbamoyl-phosphate synthase (ammonia) activity
• GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016597 amino acid binding
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006221 pyrimidine nucleotide biosynthetic process
• GO:0006526 L-arginine biosynthetic process
• GO:0006541 glutamine metabolic process
• GO:0008652 amino acid biosynthetic process
• GO:0019856 pyrimidine nucleobase biosynthetic process
• GO:0044205 'de novo' UMP biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005951 carbamoyl-phosphate synthase complex

External links

• PDB: RCSB:1jdb, PDBe:1jdb, PDBj:1jdb
• PDBsum: 1jdb
• PubMed: 10089390
• UniProt: P00968|CARB_ECOLI Carbamoyl phosphate synthase large chain (Gene Name=carB)