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BioLiP

Structure of PDB 7d0j Chain 3 Binding Site BS07

Receptor Information

>7d0j Chain 3 (length=203) Species: 3055 (Chlamydomonas reinhardtii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

LPGDFGFDPLGLLDPVNSGGFIEPKWLQYSEVIHARWAMLGAAGCIAPEV
LGAAGLIPDATNIKWFESGVIPPAGSYNGYWADPYTIFFVEIVAMQFAEL
RRLQDFRYPGSMGQQYFLGLEAIFKGSGDAAYPGGPFFNLFNLGKTEAAM
KELKLKEIKNGRLAMLAMLGYGAQAVMTGKGPFQNLVEHLADPVNNNILT
NFA

Ligand information

Ligand ID

CHL

InChI

InChI=1S/C55H71N4O6.Mg/c1-12-38-35(8)42-27-43-36(9)40(23-24-48(61)65-26-25-34(7)22-16-21-33(6)20-15-19-32(5)18-14-17-31(3)4)52(58-43)50-51(55(63)64-11)54(62)49-37(10)44(59-53(49)50)28-46-39(13-2)41(30-60)47(57-46)29-45(38)56-42;/h12,25,27-33,36,40,51H,1,13-24,26H2,2-11H3,(H-,56,57,58,59,60,62);/q-1;+4/p-1/b34-25+;/t32-,33-,36?,40?,51-;/m1./s1

InChIKey

MWVCRINOIIOUAU-UYSPMESUSA-M

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.7	CCC1=C(c2cc3c(c(c4n3[Mg]56[n+]2c1cc7n5c8c(c9[n+]6c(c4)C(C9CCC(=O)OCC=C(C)CCCC(C)CCCC(C)CCCC(C)C)C)C(C(=O)c8c7C)C(=O)OC)C)C=C)C=O
OpenEye OEToolkits 2.0.7	CCC1=C(c2cc3c(c(c4n3[Mg]56[n+]2c1cc7n5c8c(c9[n+]6c(c4)C(C9CCC(=O)OC/C=C(\C)/CCC[C@H](C)CCC[C@H](C)CCCC(C)C)C)[C@H](C(=O)c8c7C)C(=O)OC)C)C=C)C=O
CACTVS 3.385	CCC1=C(C=O)C2=Cc3n4c(C=C5[CH](C)[CH](CCC(=O)OCC=C(C)CCC[CH](C)CCC[CH](C)CCCC(C)C)C6=[N+]5[Mg]47[N]8C(=CC1=[N+]27)C(=C9C(=O)[CH](C(=O)OC)C6=C89)C)c(C)c3C=C
CACTVS 3.385	CCC1=C(C=O)C2=Cc3n4c(C=C5[C@H](C)[C@H](CCC(=O)OC\C=C(/C)CCC[C@H](C)CCC[C@H](C)CCCC(C)C)C6=[N@+]5[Mg]47[N@@]8C(=CC1=[N@+]27)C(=C9C(=O)[C@H](C(=O)OC)C6=C89)C)c(C)c3C=C

Formula

C55 H70 Mg N4 O6

Name

CHLOROPHYLL B

ChEMBL

DrugBank

ZINC

PDB chain

7d0j Chain 3 Residue 306 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

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Structure summary

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PDB	7d0j Structure of photosystem I-LHCI-LHCII from the green alga Chlamydomonas reinhardtii in State 2.
Resolution	3.42 Å
Binding residue (original residue number in PDB)	R96 W97 A158 R161 R162 D165 F184 P193 F198
Binding residue (residue number reindexed from 1)	R36 W37 A98 R101 R102 D105 F124 P133 F138
Annotation score	4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3
Mon May 12 23:18:57 2025

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

/var/www/html/BioLiP/pdb.cgi in <module>()

1701 title=pdb2title(pdbid)

1702 if bs.startswith("BS"):

=> 1703 pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)

1704 else:

1705 if lig3:

pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '7d0j', asym_id = '3', bs = 'BS07', title = 'Structure of photosystem I-LHCI-LHCII from the green alga Chlamydomonas reinhardtii in State 2.'

/var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='7d0j', asym_id='3', bs='BS07', title='Structure of photosystem I-LHCI-LHCII from the green alga Chlamydomonas reinhardtii in State 2.')

1326 display_ec(ec,csaOrig,csaRenu)

1327 if go:

=> 1328 display_go(go,uniprot,pdbid,asym_id)

1329 return pubmed,uniprot

1330

global display_go = <function display_go>, go = '0009765,0016020', uniprot = '', pdbid = '7d0j', asym_id = '3'

/var/www/html/BioLiP/pdb.cgi in display_go(go='0009765,0016020', uniprot='', pdbid='7d0j', asym_id='3')

484 '''.replace("$namespace_link",namespace_link

485 ).replace("$namespace",namespace

=> 486 ).replace("$uniprot",u

487 ))

488 for l,(term,name) in enumerate(go2aspect[Aspect]):

u undefined

UnboundLocalError: local variable 'u' referenced before assignment
args = ("local variable 'u' referenced before assignment",)
with_traceback = <built-in method with_traceback of UnboundLocalError object>