Structure of PDB 5dou Chain A Binding Site BS06

Receptor Information

>5dou Chain A (length=1422) Species: 9606 (Homo sapiens)

AQTAHIVLEDGTKMKGYSFGHPSSVAGEVVFNTGLGGYPEAITDPAYKGQ
ILTMANPIIGNGGAPDTTALDELGLSKYLESNGIKVSGLLVLDYSKDYNH
WLATKSLGQWLQEEKVPAIYGVDTRMLTKIIRDKGTMLGKIEFEGQPVDF
VDPNKQNLIAEVSTKDVKVYGKGNPTKVVAVDCGIKNNVIRLLVKRGAEV
HLVPWNHDFTKMEYDGILIAGGPGNPALAEPLIQNVRKILESDRKEPLFG
ISTGNLITGLAAGAKTYKMSMANRGQNQPVLNITNKQAFITAQNHGYALD
NTLPAGWKPLFVNVNDQTNEGIMHESKPFFAVQFHPEVTPGPIDTEYLFD
SFFSLIKKGKATTITSVLPKPALVASRVEVSKVLILGSGGLSIGQAGEFD
YSGSQAVKAMKEENVKTVLMNPNIASVQTNEVGLKQADTVYFLPITPQFV
TEVIKAEQPDGLILGMGGQTALNCGVELFKRGVLKEYGVKVLGTSVESIM
ATEDRQLFSDKLNEINEKIAPSFAVESIEDALKAADTIGYPVMIRSAYAL
GGLGSGICPNRETLMDLSTKAFAMTNQILVEKSVTGWKEIEYEVVRDADD
NCVTVCNMENVDAMGVHTGDSVVVAPAQTLSNAEFQMLRRTSINVVRHLG
IVGECNIQFALHPTSMEYCIIEVNARLSRSSALASKATGYPLAFIAAKIA
LGIPLPEIKNVVSGKTSACFEPSLDYMVTKIPRWDLDRFHGTSSRIGSSM
KSVGEVMAIGRTFEESFQKALRMCHPSIEGFTPRLPMNKEWPSNLDLRKE
LSEPSSTRIYAIAKAIDDNMSLDEIEKLTYIDKWFLYKMRDILNMEKTLK
GLNSESMTEETLKRAKEIGFSDKQISKCLGLTEAQTRELRLKKNIHPWVK
QIDTLAAEYPSVTNYLYVTYNGQEHDVNFDDHGMMVLGCGPYHIGSSVEF
DWCAVSSIRTLRQLGKKTVVVNCNPETVSTDFDECDKLYFEELSLERILD
IYHQEACGGCIISVGGQIPNNLAVPLYKNGVKIMGTSPLQIDRAEDRSIF
SAVLDELKVAQAPWKAVNTLNEALEFAKSVDYPCLLRMNVVFSEDPVVLT
KFVEGAREVEMDAVGKDGRVISHAISEHVEDAGVHSGDATLMLPTQTISQ
GAIEKVKDATRKIAKAFAISGPFNVQFLVKGNDVLVIECNLRASRSFPFV
SKTLGVDFIDVATKVMIGENVDEKHLPTLDHPIIPADYVAIKAPMFSWPR
LRDADPILRCEMASTGEVACFGEGIHTAFLKAMLSTGFKIPQKGILIGIQ
QSFRPRFLGVAEQLHNEGFKLFATEATSDWLNANNVPATPVAWPSQEGQN
PSLSSIRKLIRDGSIDLVINLPNNNTKFVHDNYVIRRTAVDSGIPLLTNF
QVTKLFAEAVQKDSKSLFHYRQ

Ligand information

• Ligand ID: NLG
• InChI: InChI=1S/C7H11NO5/c1-4(9)8-5(7(12)13)2-3-6(10)11/h5H,2-3H2,1H3,(H,8,9)(H,10,11)(H,12,13)/t5-/m0/s1
• InChIKey: RFMMMVDNIPUKGG-YFKPBYRVSA-N
• SMILES:
  ACDLabs 10.04: O=C(NC(C(=O)O)CCC(=O)O)C
  OpenEye OEToolkits 1.5.0: CC(=O)N[C@@H](CCC(=O)O)C(=O)O
  CACTVS 3.341: CC(=O)N[C@@H](CCC(O)=O)C(O)=O
  CACTVS 3.341: CC(=O)N[CH](CCC(O)=O)C(O)=O
  OpenEye OEToolkits 1.5.0: CC(=O)NC(CCC(=O)O)C(=O)O
• Formula: C7 H11 N O5
• Name: N-ACETYL-L-GLUTAMATE
• ChEMBL: CHEMBL1234751
• DrugBank: DB04075
• ZINC: ZINC000001532704
• PDB chain: 5dou Chain A Residue 2010

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dou Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): I1366 Q1367 T1391 A1393 T1394 W1410 L1438 T1443 K1444 N1449
• Binding residue (residue number reindexed from 1): I1299 Q1300 T1324 A1326 T1327 W1343 L1371 T1376 K1377 N1382
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): S294 H377 E379 R547 R587 N618 E631 H659 N698 Q700 E714 N716 R718 S722 G922 A1048 R1129 E1175 K1183 Q1243 E1255 N1257 R1262 R1319
• Catalytic site (residue number reindexed from 1): S252 H335 E337 R505 R545 N576 E589 H617 N656 Q658 E672 N674 R676 S680 G880 A1006 R1087 E1108 K1116 Q1176 E1188 N1190 R1195 R1252
• Enzyme Commision number: 6.3.4.16: carbamoyl-phosphate synthase (ammonia).

Gene Ontology

Molecular Function

• GO:0004087 carbamoyl-phosphate synthase (ammonia) activity
• GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
• GO:0004175 endopeptidase activity
• GO:0005509 calcium ion binding
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0005543 phospholipid binding
• GO:0016595 glutamate binding
• GO:0016874 ligase activity
• GO:0030955 potassium ion binding
• GO:0036094 small molecule binding
• GO:0044877 protein-containing complex binding
• GO:0046872 metal ion binding
• GO:0072341 modified amino acid binding

Biological Process

• GO:0000050 urea cycle
• GO:0001889 liver development
• GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
• GO:0006541 glutamine metabolic process
• GO:0007494 midgut development
• GO:0009410 response to xenobiotic stimulus
• GO:0009636 response to toxic substance
• GO:0010043 response to zinc ion
• GO:0014075 response to amine
• GO:0019240 citrulline biosynthetic process
• GO:0019433 triglyceride catabolic process
• GO:0019637 organophosphate metabolic process
• GO:0032094 response to food
• GO:0032496 response to lipopolysaccharide
• GO:0033762 response to glucagon
• GO:0034201 response to oleic acid
• GO:0042311 vasodilation
• GO:0042594 response to starvation
• GO:0043200 response to amino acid
• GO:0044344 cellular response to fibroblast growth factor stimulus
• GO:0046209 nitric oxide metabolic process
• GO:0048545 response to steroid hormone
• GO:0050667 homocysteine metabolic process
• GO:0051384 response to glucocorticoid
• GO:0051591 response to cAMP
• GO:0055081 monoatomic anion homeostasis
• GO:0060416 response to growth hormone
• GO:0070365 hepatocyte differentiation
• GO:0070409 carbamoyl phosphate biosynthetic process
• GO:0071242 cellular response to ammonium ion
• GO:0071320 cellular response to cAMP
• GO:0071377 cellular response to glucagon stimulus
• GO:0071400 cellular response to oleic acid
• GO:0071548 response to dexamethasone

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005759 mitochondrial matrix
• GO:0005886 plasma membrane
• GO:0032991 protein-containing complex
• GO:0042645 mitochondrial nucleoid

External links

• PDB: RCSB:5dou, PDBe:5dou, PDBj:5dou
• PDBsum: 5dou
• PubMed: 26592762
• UniProt: P31327|CPSM_HUMAN Carbamoyl-phosphate synthase [ammonia], mitochondrial (Gene Name=CPS1)