Structure of PDB 6jbj Chain A Binding Site BS01

Receptor Information
>6jbj Chain A (length=565) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RPRLDLQFLQRFLQILKVLFPSWSSQNALMFLTLLCLTLLEQFVIYQVGL
IPSQYYGVLGNKDLEGFKTLTFLAVMLIVLNSTLKSFDQFTCNLLYVSWR
KDLTEHLHRLYFRGRAYYTLNVLRDDIDNPDQRISQDVERFCRQLSSMAS
KLIISPFTLVYYTYQCFQSTGWLGPVSIFGYFILGTVVNKTLMGPIVMKL
VHQEKLEGDFRFKHMQIRVNAEPAAFYRAGHVEHMRTDRRLQRLLQTQRE
LMSKELWLYIGINTFDYLGSILSYVVIAIPIFSGVYGDLSPAELSTLVSK
NAFVCIYLISCFTQLIDLSTTLSDVAGYTHRIGQLRETLLDMSLDTAFLL
ERVSISAPSSDKPLIKDLSLKISEGQSLLITGNTGTGKTSLLRVLGGLWT
STRGSVQMLTDFGPHGVLFLPQKPFFTDGTLREQVIYPLKEVYPDSGSAD
DERILRFLELAGLSNLVARTEGLDQQVDWNWYDVLSPGEMQRLSFARLFY
LQPKYAVLDQATSALTEEVESELYRIGQQLGMTFISVGHRQSLEKFHSLV
LKLCGGGRWELMRIK
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain6jbj Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6jbj Cryo-EM structure of human lysosomal cobalamin exporter ABCD4.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		T423 G424 G426 K427 T428 R432 W438 Q461
Binding residue
(residue number reindexed from 1)		T384 G385 G387 K388 T389 R393 W399 Q422
Annotation score5
Enzymatic activity
Enzyme Commision number 7.6.2.8: ABC-type vitamin B12 transporter.
Gene Ontology
Molecular Function
GO:0005324 long-chain fatty acid transmembrane transporter activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0015420 ABC-type vitamin B12 transporter activity
GO:0016887 ATP hydrolysis activity
GO:0042626 ATPase-coupled transmembrane transporter activity
GO:0042802 identical protein binding
GO:0140359 ABC-type transporter activity
Biological Process
GO:0006635 fatty acid beta-oxidation
GO:0007031 peroxisome organization
GO:0009235 cobalamin metabolic process
GO:0015889 cobalamin transport
GO:0015910 long-chain fatty acid import into peroxisome
GO:0042760 very long-chain fatty acid catabolic process
GO:0055085 transmembrane transport
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005777 peroxisome
GO:0005778 peroxisomal membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0043190 ATP-binding cassette (ABC) transporter complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6jbj, PDBe:6jbj, PDBj:6jbj
PDBsum6jbj
PubMed31467407
UniProtO14678|ABCD4_HUMAN Lysosomal cobalamin transporter ABCD4 (Gene Name=ABCD4)

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