Structure of PDB 7sqc Chain 1D Binding Site BS01

Receptor Information

>7sqc Chain 1D (length=1686) Species: 3055 (Chlamydomonas reinhardtii)

YEDLAGLVLPPETQMFLDTWKRPEELVLNSPDVPMVTLEGSLQAGHRTFE
WLQAVFVMVISAQKAPNGKYKIKLYIMDAWRTVVVDDRIPVDLFGRPLLV
NARPIQLWPLLLSKAVLKVLAANRILHCGLPHQAAAFQLLTGTERHAVAA
VTLVKRALPERPPPRLIVLVGPSGVGRGALLQRLVGELPDKFGLTVSHTT
RPPREHEVQGGDYFFCLENAPVPSANDGVHLYGTSFATVREVAATGKLCL
MGLDVQGVRSLRANKRIDGLYVFVSPPSLDELERRQRGRLKEAETTIAKR
LAWARAELDKKPVVITGPTTGERRALMEQLVREFPDVFAYPRHTTTRPAS
PTEFTSAARSGALLEHHTELFKHPLVTRQWGVTADAIKEVIRAGRLPLME
CETEGAEMLKKRGIDCLTLFLKPPSMDVFETRLRDHLTETDEEIAARLDM
ARREMEAAAAAGSPFDATIVNDDPEAAYAELTRLISQPVLVLCGPSAAGR
SALAKQLLSTFPDKFTAPGITTDRKPTKGEISTAACTFVGPKDLVKMQAE
GLIAYMRAPEEKGAGTTAITNAALLRVAGENKVAVLELPDGGAVVPELRK
GAVLKDALYVFVASAALAELDTQAGGAASSGELYDTVVREDDIMDLISAV
RMALAAHVPNVVPPPYRPLVVAGAFGTGKRKLLARLFDALPGRFAVPVIT
TTRQVLGEVYGITVAAVKKVGASGRVPIIEVDHVEDAAALRARGFDAAYL
FIGMEDMGKLFHVINEELSANPPLGYELQDAVNQFFAAAKAEMAASRQPG
LFDEWVHHVHDAPDPSFIRLAEAVHRSYLKVMVLGPAASGKSTQCDMLAA
HFGMPHVNVGDLLFEEVRKKTPLGLEAKEYMDASKTVPDRFFFEVLTQRL
AEPDCVARGWLLDGFPHTAEQCEELGRRGISPDKVLLLEGEHAVLLDRSR
YRRYDPATGKVYHMPDAEVVARLVPRHDDSDENVSARLALSDAHVAALRD
AYEDICLRLNSTSDPRVMFQQALDYLTLEARVPELAVVPSTQDPALFPTS
HQLRRVDTGKLSRVALLYVDSPEPVKLLSSLFTGPQYGLLEDPPTPRNVL
VLAGPAGVGKTAVLRMLLQQLGEQLELVPVVTSRLDAMEDAEAAGQLLGT
CEGWDGHRYGVSRAALQAAWAAGKLPVVEGPLELALALKELNSVMVPLLL
SARVVYLAVDVAEQDVRLRLQDQREEAAVGVCIAAAVREAETIRAMQKAL
DDHAAAVLDVVMQATDAVVAFHAAKRLAADSWRRPRAQVAGQLVLEAFDW
RPGRTVQRLRTLMANAGLLELPRGRHVLRINSDPLFLHAVTFMSSTPCTV
GEYSQVMPLCAPEAHVVPLEGRYGEAPAGAVGVLFRYCFALHQAATLSAY
LSINGEDMRAATRLLLMDRASGVARPVPSNRLHATELPASGAGYCLLALY
DTGSRGVNEEGTYCLTVTCTSPLALTEVPCHRLDSFVEAYRPNSRATLSR
HVITCTTTTQLALVAAAEPRLPFRLTLQEAPTGREITWLTSPDYPTLVSA
APVPDGFALVADVTLKPGKYLVSCTLDAADCPAGMQPDPRTGALPEGAEP
VKLRLWVAPSADEKSCTVLADNARQAAATQAAASEGAARLASVGAALQAS
KGERAGFKQRQANNFAEWRASLMAAQREAASKRHEL

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: 7sqc Chain 1D Residue 2601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7sqc Ciliary central apparatus structure reveals mechanisms of microtubule patterning.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): A1585 V1587 G1588 K1589 T1590 R1811 L1814 Q1815
• Binding residue (residue number reindexed from 1): A1106 V1108 G1109 K1110 T1111 R1217 L1220 Q1221
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.7.4.3: adenylate kinase.

Gene Ontology

Molecular Function

• GO:0004017 adenylate kinase activity
• GO:0004198 calcium-dependent cysteine-type endopeptidase activity
• GO:0004385 guanylate kinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0016887 ATP hydrolysis activity
• GO:0019205 nucleobase-containing compound kinase activity

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process
• GO:0006508 proteolysis
• GO:0016310 phosphorylation
• GO:0046037 GMP metabolic process
• GO:0046710 GDP metabolic process
• GO:0046940 nucleoside monophosphate phosphorylation

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:7sqc, PDBe:7sqc, PDBj:7sqc
• PDBsum: 7sqc
• PubMed: 35578023
• UniProt: A0A2K3D425