Structure of PDB 4hat Chain C Binding Site BS01

Receptor Information

>4hat Chain C (length=1017) Species: 4932 (Saccharomyces cerevisiae)

GAMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAW
QKADQILQFSTNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMI
ISMCQDDEVFKTQKNLINKSDLTLVQILKQEWPQNWPEFIPELIGSSSSS
VNVCENNMIVLKLLSEEVFDFSAEQMTQAKALHLKNSMSKEFEQIFKLCF
QVLEQGASSSLIVATLESLLRYLHWIPYRYIYETNILELLSTKFMTSPDT
RAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLK
ATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLI
QLSKIEERELFKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENM
VRPEEVLVVENDEGEIVREFVKESDTIQLYKSEREVLVYLTHLNVIDTEE
IMISKLARQIDGSEWSWHNINTLSWAIGSISGTMSEDTEKRFVVTVIKDL
LDLCVKKRGKDNKAVVASDIMYVVGQYPRFLKAHWNFLRTVILKLFEFMH
ETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTAD
LQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTA
NPTLLLDSETVKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAV
SSMISAQVAAEGLIATKTPKVRGLRTIKKEILKLVETYISKARNLDDVVK
VLVEPLLNAVLEDYMNNVPDARDAEVLNCMTTVVEKVGHMIPQGVILILQ
SVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFLELPPAAFKLF
VDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIF
VSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQEAEVPQGT
SNQVYLSQYLANMLSNAFPHLTSEQIASFLSALTKQCKDLVVFKGTLRDF
LVQIKEVGGDPTDYLFA

Ligand information

• Ligand ID: LMB
• InChI: InChI=1S/C33H52O7/c1-9-28(14-15-29(34)24(5)13-16-30(35)36)19-22(3)12-10-11-21(2)17-25(6)32(39)27(8)33(40)26(7)18-23(4)20-31(37)38/h10-11,14-15,17,19-20,22,24-27,29,33-34,40H,9,12-13,16,18H2,1-8H3,(H,35,36)(H,37,38)/b11-10+,15-14+,21-17+,23-20+,28-19-/t22-,24+,25-,26+,27-,29+,33-/m1/s1
• InChIKey: GCBBLAVMGONVHO-XYERBDPFSA-N
• SMILES:
  ACDLabs 12.01: O=C(O)CCC(C)C(O)/C=C/C(=C\C(C)C/C=C/C(=C/C(C(=O)C(C)C(O)C(C)CC(=C\C(=O)O)\C)C)C)CC
  CACTVS 3.370: CCC(C=C[CH](O)[CH](C)CCC(O)=O)=C[CH](C)CC=CC(C)=C[CH](C)C(=O)[CH](C)[CH](O)[CH](C)CC(C)=CC(O)=O
  CACTVS 3.370: CCC(/C=C/[C@H](O)[C@@H](C)CCC(O)=O)=C/[C@H](C)C/C=C/C(C)=C/[C@@H](C)C(=O)[C@@H](C)[C@H](O)[C@@H](C)CC(/C)=C/C(O)=O
  OpenEye OEToolkits 1.7.6: CCC(=CC(C)CC=CC(=CC(C)C(=O)C(C)C(C(C)CC(=CC(=O)O)C)O)C)C=CC(C(C)CCC(=O)O)O
  OpenEye OEToolkits 1.7.6: CC/C(=C/[C@H](C)C/C=C/C(=C/[C@@H](C)C(=O)[C@@H](C)[C@@H]([C@@H](C)C/C(=C/C(=O)O)/C)O)/C)/C=C/[C@@H]([C@@H](C)CCC(=O)O)O
• Formula: C33 H52 O7
• Name: Leptomycin B, bound form
• ZINC: ZINC000098209119
• PDB chain: 4hat Chain C Residue 1101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4hat Nuclear export inhibition through covalent conjugation and hydrolysis of Leptomycin B by CRM1.
• Resolution: 1.78 Å
• Binding residue (original residue number in PDB): K525 V529 C539 K548 A552 I555 F572 T575 K579
• Binding residue (residue number reindexed from 1): K490 V494 C504 K513 A517 I520 F537 T540 K544
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005049 nuclear export signal receptor activity
• GO:0005515 protein binding
• GO:0017070 U6 snRNA binding
• GO:0030619 U1 snRNA binding
• GO:0030620 U2 snRNA binding
• GO:0030621 U4 snRNA binding
• GO:0030623 U5 snRNA binding
• GO:0031267 small GTPase binding
• GO:0061608 nuclear import signal receptor activity

Biological Process

• GO:0000055 ribosomal large subunit export from nucleus
• GO:0000056 ribosomal small subunit export from nucleus
• GO:0006406 mRNA export from nucleus
• GO:0006409 tRNA export from nucleus
• GO:0006611 protein export from nucleus
• GO:0006886 intracellular protein transport
• GO:0015031 protein transport
• GO:0034501 protein localization to kinetochore
• GO:0051168 nuclear export
• GO:0051170 import into nucleus
• GO:0071528 tRNA re-export from nucleus

Cellular Component

• GO:0000776 kinetochore
• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005816 spindle pole body
• GO:0048471 perinuclear region of cytoplasm

External links

• PDB: RCSB:4hat, PDBe:4hat, PDBj:4hat
• PDBsum: 4hat
• PubMed: 23297231
• UniProt: P30822|XPO1_YEAST Exportin-1 (Gene Name=CRM1)