Structure of PDB 7dco Chain A

Receptor sequence

>7dcoA (length=2205) Species: 4932 (Saccharomyces cerevisiae)

LYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLL
ENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRR
EKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYV
KDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKN
YYYLFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFR
VPIRSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDP
SLNPIDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMVR
AQDVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNKT
KLLKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLDY
NFNLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNVD
AFQLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKNL
GKGPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEIVKTT
TKQRLDAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWRCWKA
NIPWDVPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTMV
KKNLGRLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLESRSF
SPIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAYD
NPHDTLNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKITDAYL
DQYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRGQ
SAVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKDM
SHVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEFM
QFKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPNF
ENSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWEN
AFVSVYSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTKQ
RTAKAYLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFTY
FREAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKELG
GLGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYIT
TWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTLF
QRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRTD
VIQALGGIETILEHTLFKGTGFNSWEGLFWEKASGFEDSMQFKKLTHAQR
TGLSQIPNRRFTLWWSPTINRANVYVGFLVQLDLTGIFLHGKIPTLKISL
IQIFRAHLWQKIHESIVFDICQILDGELDVLQIESVTKETVHPRKSYKMN
SSAADITMESVHEWEVSKPSLLHETNDSFKGLITNKMWFDVQLRYGDYDS
HDISRYVRAKFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLK
PLIQNSMRTIMKANPALYVLRERIRKGLQIYQSSVQEPFLNSSNYAELFN
NDIKLFVDDTNVYRVTVHKTFEGNVATKAINGCIFTLNPKTGHLFLKIIH
TSVWAGQKRLSQLAKWKTAEEVSALVRSLPKEEQPKQIIVTRKAMLDPLE
VHMLDFPNIAIRPTELRLPFSAAMSIDKLSDVVMKATEPQMVLFNIYDDW
LDRISSYTAFSRLTLLLRALKTNEESAKMILLSDPTITIKSYHLWPSFTD
EQWITIESQMRDLILTEYGRKYNVNISALTQTEIKDIILGKNEWRKSAIA
NTLLYLRLKNIYVSADDFVEEQNVYVLPKNLLKKFIEISDVKIQVAAFIY
GMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIGDLPDTEGLELLGW
IHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFSTPGSVSLSAYNLT
DEGYQWGEENKDIMNVLSEGFEPTFSTHAQLLLSDRITGNFIIPSGNVWN
YTFMGTAFNQEGDYNFKYGIPLEFYNEMHRPVHFLQFSELAGDEELEAEQ
IDVFS

3D structure

• PDB: 7dco Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2.
• Chain: A
• Resolution: 2.5 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	Y128 K190 T205 R207 R284 G295 T296 S297 K299 K334 K340 E353 R358 W402 F484 R488 R495 D498 K503 K527 H535 T537 P539 N541 N543 K549 K670 Y671 K672 H675 R709 N713 R716 G717 P720 H839 N1369 R1370 L1373	Y2 K64 T79 R81 R158 G169 T170 S171 K173 K208 K214 E227 R232 W276 F339 R343 R350 D353 K358 K382 H390 T392 P394 N396 N398 K404 K525 Y526 K527 H530 R564 N568 R571 G572 P575 H694 N1224 R1225 L1228
BS02	rna	A	S151 T606 E609 K611 R614 G616 S618 Y725 N728 R732 R737 K743 T744 T746 Q748 R749 A752 Y753 L756 H1592	S25 T461 E464 K466 R469 G471 S473 Y580 N583 R587 R592 K598 T599 T601 Q603 R604 A607 Y608 L611 H1447
BS03	rna	A	K351 T607 R610 K611 R614 R668 Y671 K1378 M1379 H1424 T1430	K225 T462 R465 K466 R469 R523 Y526 K1233 M1234 H1279 T1285
BS04	rna	A	D755 R759 K777 Q784 S787 K794 K847 R851 R854 N930 A931 R934 K1093 D1094 R1595	D610 R614 K632 Q639 S642 K649 K702 R706 R709 N785 A786 R789 K948 D949 R1450
BS05	peptide	A	N343 E353 P354 E359 R380 S381 E382 K1362 D1411 T1423 H1424 F1425 R1426 A1427 G1428	N217 E227 P228 E233 R254 S255 E256 K1217 D1266 T1278 H1279 F1280 R1281 A1282 G1283
BS06	IHP	A	R236 K517 H659 K681 K684 H685 Y688 K697	R110 K372 H514 K536 K539 H540 Y543 K552

Gene Ontology

--> -->

UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 29 10:43:03 2024

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>()

   1443                 pubmed=display_regular_ligand(pdbid,asym_id,lig3,ligIdx,title)

   1444         else:

=> 1445             pubmed,uniprot=display_protein_receptor(pdbid,asym_id,title)

   1446     

   1447     uniprot_line=''

pubmed = '', uniprot = '', display_protein_receptor = <function display_protein_receptor>, pdbid = '7dco', asym_id = 'A', title = 'Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2.'

 /var/www/html/BioLiP/pdb.cgi in display_protein_receptor(pdbid='7dco', asym_id='A', title='Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2.')

    839 

    840     if go:

=>  841         display_go(go,uniprot,pdbid,asym_id)

    842     return pubmed,uniprot

    843 

global display_go = <function display_go>, go = '0000398,0003723,0005681,0008233,0008237,0017070,0030623', uniprot = '', pdbid = '7dco', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000398,0003723,0005681,0008233,0008237,0017070,0030623', uniprot='', pdbid='7dco', asym_id='A')

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

    481           ).replace("$namespace",namespace

=>  482           ).replace("$uniprot",u

    483         ))

    484         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>