Structure of PDB 1bxr Chain E Binding Site BS06

Receptor Information
>1bxr Chain E (length=1073) 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
AVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPV
LLDHFLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYT
LSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLIEVNPRAARTV
PFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF
PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVR
EGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPH
IQDRIKNGEYTYIINTTSGRRAIEDSRVIRRSALQYKVHYDTTLNGGFAT
AMALNADATEKVISVQEMHAQIK
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 chain1bxr Chain E Residue 2920 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1bxr Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		E783 D791 E892 Y1040 D1041 T1042
Binding residue
(residue number reindexed from 1)		E783 D791 E892 Y1040 D1041 T1042
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) R129 R169 M174 G176 K202 E215 H243 N283 Q285 E299 N301 R303 S307 D338 G507 K634 R715 G721 G722 S745 E761 D769 Q829 E841 N843 R848 P901
Catalytic site (residue number reindexed from 1) R129 R169 M174 G176 K202 E215 H243 N283 Q285 E299 N301 R303 S307 D338 G507 K634 R715 G721 G722 S745 E761 D769 Q829 E841 N843 R848 P901
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1bxr, PDBe:1bxr, PDBj:1bxr
PDBsum1bxr
PubMed10029528
UniProtP00968|CARB_ECOLI Carbamoyl phosphate synthase large chain (Gene Name=carB)

[Back to BioLiP]