Structure of PDB 4pkd Chain B Binding Site BS01

Receptor Information

>4pkd Chain B (length=240) Species: 9606,9823

TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQA
FVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVEET
REERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNY
DTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK
HADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRG

Ligand information

>4pkd Chain V (length=55)

ggauccauugcacuccggauccaggagauaccaugaucacgaaggugguu
uuccu

<<<<<<..........>>>>>><<<<<<.<<<<<..........>>>>>>
>>>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4pkd Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): Y13 N15 N16 E19 K22 K23 R47 S48 L49 K50 M51 R52 Q54 F56 K80 Q85 K88 D90 S91 D92 R136 K139 R143 W154 D159 N161 A162 F171 A173 R174 V175 N176 Y177 H198 Y201 S202 K203 R204 R209 Y211 F213 R237 L240 D242 E244 R245 G246 W252 P254 R255 R256 G258 L261 G262 T264 R265 G267
• Binding residue (residue number reindexed from 1): Y8 N10 N11 E14 K17 K18 R42 S43 L44 K45 M46 R47 Q49 F51 K75 Q80 K83 D85 S86 D87 R109 K112 R116 W127 D132 N134 A135 F144 A146 R147 V148 N149 Y150 H171 Y174 S175 K176 R177 R182 Y184 F186 R210 L213 D215 E217 R218 G219 W225 P227 R228 R229 G231 L234 G235 T237 R238 G240

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0030619 U1 snRNA binding

External links

• PDB: RCSB:4pkd, PDBe:4pkd, PDBj:4pkd
• PDBsum: 4pkd
• PubMed: 25555158
• UniProt: P08621|RU17_HUMAN U1 small nuclear ribonucleoprotein 70 kDa (Gene Name=SNRNP70);
  Q06AA4