Structure of PDB 4pmw Chain B Binding Site BS01

Receptor Information

>4pmw Chain B (length=691) Species: 10090 (Mus musculus)

IFETYMSKEDVSEGLKRGTLIQGVLRINPKKFHEAFIPSPDGDRDIFIDG
VVARNRALNGDLVVVKLLPEKSAKVVYILEKKHSRAATGILKLLFKKYAL
FSPSDHRVPRIYVPLKDCPQDFMTRPKDFANTLFICRIIDWKEDCNFALG
QLAKSLGQAGEIEPETEGILTEYGVDFSDFSSEVLECLPQSLPWTIPPDE
VGKRRDLRKDCIFTIDPSTARDLNDALACRRLTDGTFEVGVHIADVSYFV
PEGSSLDKVAAERATSVYLVQKVVPMLPRLLCEELCSLNPMTDKLTFSVI
WKLTPEGKILEEWFGRTIIRSCTKLSYDHAQSMIENPTEKIPEEELPPIS
PEHSVEEVHQAVLNLHSIAKQLRRQRFVDGALRLDQLKLAFTLDHETGLP
QGCHIYEYRDSNKLVEEFMLLANMAVAHKIFRTFPEQALLRRHPPPQTKM
LSDLVEFCDQMGLPMDVSSAGALNKSLTKTFGDDKYSLARKEVLTNMYSR
PMQMALYFCSGMLQDQEQFRHYALNVPLYTHFTSPIRRFADVIVHRLLAA
ALGYSEQPDVEPDTLQKQADHCNDRRMASKRVQELSIGLFFAVLVKESGP
LESEAMVMGVLNQAFDVLVLRFGVQKRIYCNALALRSYSFQKVGKKPELT
LVWEPDDLEEEPTQQVITIFSLVDVVLQAEATALKYSAILK

Ligand information

>4pmw Chain D (length=14)

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..............

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4pmw Mechanism of Dis3l2 substrate recognition in the Lin28-let-7 pathway.
• Resolution: 2.95 Å
• Binding residue (original residue number in PDB): R74 N76 P77 K78 F80 F84 D93 H271 R275 D381 P382 A385 D387 L388 N389 D390 Y433 Y492 L549 D550 Q551 K553 Y573 E581 M584 R606 H608 Q612 M615 S664 R665 M667 M669 A670 H686 Y694 H696 T698 S699 R702 R741 K745 R746 L776 N777 Q778 Q790 R792 Y794 N796
• Binding residue (residue number reindexed from 1): R26 N28 P29 K30 F32 F36 D45 H106 R110 D216 P217 A220 D222 L223 N224 D225 Y268 Y327 L384 D385 Q386 K388 Y408 E416 M419 R441 H443 Q447 M450 S499 R500 M502 M504 A505 H521 Y529 H531 T533 S534 R537 R576 K580 R581 L611 N612 Q613 Q625 R627 Y629 N631
• Binding affinity: PDBbind-CN: Kd=9pM

Enzymatic activity

• Catalytic site (original residue number in PDB): D381 D387 N389 D390 Y492 R702
• Catalytic site (residue number reindexed from 1): D216 D222 N224 D225 Y327 R537
• Enzyme Commision number: 3.1.13.-

Gene Ontology

Molecular Function

• GO:0000175 3'-5'-RNA exonuclease activity
• GO:0003723 RNA binding
• GO:0004540 RNA nuclease activity

External links

• PDB: RCSB:4pmw, PDBe:4pmw, PDBj:4pmw
• PDBsum: 4pmw
• PubMed: 25119025
• UniProt: Q8CI75|DI3L2_MOUSE DIS3-like exonuclease 2 (Gene Name=Dis3l2)