Structure of PDB 1jdb Chain B Binding Site BS10

Receptor Information
>1jdb Chain B (length=1057) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSN
PATIMTDPEMADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCAL
ELERQGVLEEFGVTMIGATADAIDKAEDRRRFDVAMKKIGLETARSGIAH
TMEEALAVAADVGFPCIIRPSFTMGGSGGGIAYNREEFEEICARGLDLSP
TKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAMGIHTGDSITV
APAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM
NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEP
SIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALR
GLEVGATGFDPKVSLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVD
GVFNLTNIDRWFLVQIEELVRLEEKVAEVGITGLNADFLRQLKRKGFADA
RLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDTAYMYSTYEEE
CEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN
CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKL
ARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEM
AVEKAKEIGYPLVVRAMEIVYDEADLRRYFQTAVLLDHFLDDAVEVDVDA
ICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKL
AFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAA
RVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGE
VMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLLK
QGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINT
TSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQ
EMHAQIK
Ligand information
Ligand IDORN
InChIInChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1
InChIKeyAHLPHDHHMVZTML-BYPYZUCNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C(C[C@@H](C(=O)O)N)CN
CACTVS 3.370NCCC[CH](N)C(O)=O
CACTVS 3.370NCCC[C@H](N)C(O)=O
ACDLabs 12.01O=C(O)C(N)CCCN
OpenEye OEToolkits 1.7.6C(CC(C(=O)O)N)CN
FormulaC5 H12 N2 O2
NameL-ornithine
ChEMBLCHEMBL446143
DrugBankDB00129
ZINCZINC000001532530
PDB chain1jdb Chain B Residue 1095 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1jdb The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		E782 D790 E891 V892 L906 Y1039 D1040 T1041
Binding residue
(residue number reindexed from 1)		E767 D775 E876 V877 L891 Y1024 D1025 T1026
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) R128 R168 G174 S176 K201 E214 H242 N282 Q284 F285 E298 M299 N300 P301 R302 S307 D337 G506 K633 R714 E760 D768 Q828 E840 N842 R847 P900
Catalytic site (residue number reindexed from 1) R129 R169 G175 S177 K202 E215 H243 N283 Q285 F286 E299 M300 N301 P302 R303 S308 D338 G507 K634 R715 E745 D753 Q813 E825 N827 R832 P885
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1jdb, PDBe:1jdb, PDBj:1jdb
PDBsum1jdb
PubMed10089390
UniProtP00968|CARB_ECOLI Carbamoyl phosphate synthase large chain (Gene Name=carB)

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