8FD7: PDB entry 8FD7

Structure of the human L-type voltage-gated calcium channel Cav1.2 complexed with gabapentin. Determined by electron microscopy at 3.1 Å resolution. Released 22 Mar 2023.

Method
Electron microscopy
Resolution
3.1 Å
Organisms
Oryctolagus cuniculus, Homo sapiens
Chains
3
Atoms
19,701
Mol. weight
370.95 kDa
Ligands
WO9, CA, GBN, NAG
Released
22 Mar 2023

Explore 8FD7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FD7 contains 108 α-helices and 67 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain C: 7 helices, 7 β-strands

ElementResiduesLengthSheet
β-strand180-183419
α-helix191-20717
β-strand209120
β-strand212120
β-strand213-216421
α-helix241-2444
α-helix247-26216
β-strand267-270421
α-helix277-2804
β-strand288-292519
α-helix297-3059
α-helix312-32615
β-strand335-337319
α-helix342-36019
Chain D: 38 helices, 53 β-strands
ElementResiduesLengthSheet
α-helix32-5423
α-helix56-6611
β-strand70-7451
α-helix77-11135
β-strand124-12632
β-strand12813
β-strand144-14632
β-strand152-15324
β-strand160-16124
β-strand16215
β-strand167-16933
α-helix179-18810
α-helix191-20111
β-strand208-21253
β-strand217-22043
β-strand22215
α-helix240-2423
α-helix244-2507
β-strand257-26156
α-helix264-2663
α-helix269-28214
β-strand29117
β-strand292-29656
β-strand300-30236
β-strand31017
α-helix314-32411
α-helix335-34511
β-strand359-36466
α-helix372-3787
β-strand385-39176
α-helix399-4079
β-strand411-41556
α-helix418-4203
α-helix428-4314
α-helix434-4396
α-helix440-4434
β-strand447-44823
β-strand452-45323
β-strand460-469103
α-helix482-4843
β-strand486-495103
α-helix496-5005
β-strand513-51758
β-strand52219
β-strand523-52538
α-helix533-5353
β-strand540110
β-strand56219
α-helix563-5664
α-helix571-58111
β-strand586-595108
β-strand601111
β-strand602-613128
α-helix6141
β-strand620-62458
α-helix627-6293
β-strand631-63551
α-helix640-6489
α-helix652-6543
α-helix655-6584
α-helix681-69111
α-helix701-71717
α-helix718-7225
β-strand731-738812
β-strand743-745312
α-helix748-7536
α-helix760-7623
α-helix764-7718
β-strand775113
β-strand776-778312
α-helix779-7813
β-strand794-802912
β-strand809-8181012
α-helix820-8289
β-strand850-856714
β-strand860115
β-strand861-863314
β-strand876115
α-helix882-8887
β-strand895-9061211
β-strand909110
β-strand974-9841111
β-strand991114
β-strand994-996314
β-strand1003-1005314
β-strand1008-1009214
β-strand1013113
β-strand1015-1021714
α-helix1023-10253
β-strand1038-1040311
α-helix1045-10484
Chain K: 63 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix113-1197
α-helix124-14320
α-helix156-18126
α-helix189-21022
α-helix235-2428
α-helix243-2508
α-helix255-26511
α-helix266-2683
α-helix269-28921
β-strand299116
β-strand305116
β-strand331116
α-helix350-36011
α-helix365-37612
α-helix381-41232
α-helix421-44222
α-helix443-4475
α-helix521-5233
α-helix526-54116
α-helix553-57725
α-helix580-5845
α-helix590-60516
α-helix606-6083
α-helix614-63017
α-helix638-67235
α-helix692-70413
α-helix709-71810
α-helix724-7274
α-helix730-76233
α-helix891-8977
α-helix901-91313
α-helix914-9185
α-helix929-95022
α-helix968-97912
α-helix997-9993
α-helix1003-10086
α-helix1018-102912
α-helix1031-105020
β-strand1056-1058317
β-strand1072-1075418
β-strand1085-1088418
β-strand1091-1093317
α-helix1105-11128
α-helix1117-11259
α-helix1143-117028
α-helix1184-11929
α-helix1219-123517
α-helix1236-12394
α-helix1245-127026
α-helix1275-12784
α-helix1282-130019
α-helix1330-13345
α-helix1335-13373
α-helix1338-13425
α-helix1345-135410
α-helix1360-138122
α-helix1402-141413
α-helix1418-14247
α-helix1452-148231
α-helix1486-14894
α-helix1491-150313
α-helix1514-15174
α-helix1520-15223
α-helix1540-15423
α-helix1558-156912
α-helix1578-15814
α-helix1582-15865
α-helix15871
α-helix1588-15925
α-helix1601-16088

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Voltage-dependent calcium channel subunit alpha-2/delta-1Dprotein1105Oryctolagus cuniculusP13806 (AlphaFold model)
Voltage-dependent L-type calcium channel subunit alpha-1CKprotein1648Homo sapiensQ13936 (AlphaFold model)
Voltage-dependent L-type calcium channel subunit beta-3Cprotein477Oryctolagus cuniculusP54286 (AlphaFold model)
Sequence of entity 1 (D), FASTA
>8FD7_1 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains D)
MAAGRPLAWTLTLWQAWLILIGPSSEEPFPSAVTIKSWVDKMQEDLVTLAKTASGVHQLV
DIYEKYQDLYTVEPNNARQLVEIAARDIEKLLSNRSKALVRLALEAEKVQAAHQWREDFA
SNEVVYYNAKDDLDPEKNDSEPGSQRIKPVFIDDANFRRQVSYQHAAVHIPTDIYEGSTI
VLNELNWTSALDDVFKKNREEDPSLLWQVFGSATGLARYYPASPWVDNSRTPNKIDLYDV
RRRPWYIQGAASPKDMLILVDVSGSVSGLTLKLIRTSVSEMLETLSDDDFVNVASFNSNA
QDVSCFQHLVQANVRNKKVLKDAVNNITAKGITDYKKGFSFAFEQLLNYNVSRANCNKII
MLFTDGGEERAQEIFAKYNKDKKVRVFTFSVGQHNYDRGPIQWMACENKGYYYEIPSIGA
IRINTQEYLDVLGRPMVLAGDKAKQVQWTNVYLDALELGLVITGTLPVFNITGQFENKTN
LKNQLILGVMGVDVSLEDIKRLTPRFTLCPNGYYFAIDPNGYVLLHPNLQPKPIGVGIPT
INLRKRRPNVQNPKSQEPVTLDFLDAELENDIKVEIRNKMIDGESGEKTFRTLVKSQDER
YIDKGNRTYTWTPVNGTDYSLALVLPTYSFYYIKAKIEETITQARYSETLKPDNFEESGY
TFLAPRDYCSDLKPSDNNTEFLLNFNEFIDRKTPNNPSCNTDLINRVLLDAGFTNELVQN
YWSKQKNIKGVKARFVVTDGGITRVYPKEAGENWQENPETYEDSFYKRSLDNDNYVFTAP
YFNKSGPGAYESGIMVSKAVEIYIQGKLLKPAVVGIKIDVNSWIENFTKTSIRDPCAGPV
CDCKRNSDVMDCVILDDGGFLLMANHDDYTNQIGRFFGEIDPSLMRHLVNISVYAFNKSY
DYQSVCEPGAAPKQGAGHRSAYVPSIADILQIGWWATAAAWSILQQFLLSLTFPRLLEAA
DMEDDDFTASMSKQSCITEQTQYFFDNDSKSFSGVLDCGNCSRIFHVEKLMNTNLIFIMV
ESKGTCPCDTRLLIQAEQTSDGPDPCDMVKQPRYRKGPDVCFDNNVLEDYTDCGGVSGLN
PSLWSIIGIQFVLLWLVSGSRHCLL
Sequence of entity 2 (K), FASTA
>8FD7_2 Voltage-dependent L-type calcium channel subunit alpha-1C (chains K)
MVNENTRMYIPEENHQGSNYGSPRPAHANMNANAAAGLAPEHIPTPGAALSWQAAIDAAR
QAKLMGSAGNATISTVSSTQRKRQQYGKPKKQGSTTATRPPRALLCLTLKNPIRRACISI
VEWKPFEIIILLTIFANCVALAIYIPFPEDDSNATNSNLERVEYLFLIIFTVEAFLKVIA
YGLLFHPNAYLRNGWNLLDFIIVVVGLFSAILEQATKADGANALGGKGAGFDVKALRAFR
VLRPLRLVSGVPSLQVVLNSIIKAMVPLLHIALLVLFVIIIYAIIGLELFMGKMHKTCYN
QEGIADVPAEDDPSPCALETGHGRQCQNGTVCKPGWDGPKHGITNFDNFAFAMLTVFQCI
TMEGWTDVLYWVNDAVGRDWPWIYFVTLIIIGSFFVLNLVLGVLSGEFSKEREKAKARGD
FQKLREKQQLEEDLKGYLDWITQAEDIDPENEDEGMDEEKPRNMSMPTSETESVNTENVA
GGDIEGENCGARLAHRISKSKFSRYWRRWNRFCRRKCRAAVKSNVFYWLVIFLVFLNTLT
IASEHYNQPNWLTEVQDTANKALLALFTAEMLLKMYSLGLQAYFVSLFNRFDCFVVCGGI
LETILVETKIMSPLGISVLRCVRLLRIFKITRYWNSLSNLVASLLNSVRSIASLLLLLFL
FIIIFSLLGMQLFGGKFNFDEMQTRRSTFDNFPQSLLTVFQILTGEDWNSVMYDGIMAYG
GPSFPGMLVCIYFIILFICGNYILLNVFLAIAVDNLADAESLTSAQKEEEEEKERKKLAR
TASPEKKQELVEKPAVGESKEEKIELKSITADGESPPATKINMDDLQPNENEDKSPYPNP
ETTGEEDEEEPEMPVGPRPRPLSELHLKEKAVPMPEASAFFIFSSNNRFRLQCHRIVNDT
IFTNLILFFILLSSISLAAEDPVQHTSFRNHILGNADYVFTSIFTLEIILKMTAYGAFLH
KGSFCRNYFNILDLLVVSVSLISFGIQSSAINVVKILRVLRVLRPLRAINRAKGLKHVVQ
CVFVAIRTIGNIVIVTTLLQFMFACIGVQLFKGKLYTCSDSSKQTEAECKGNYITYKDGE
VDHPIIQPRSWENSKFDFDNVLAAMMALFTVSTFEGWPELLYRSIDSHTEDKGPIYNYRV
EISIFFIIYIIIIAFFMMNIFVGFVIVTFQEQGEQEYKNCELDKNQRQCVEYALKARPLR
RYIPKNQHQYKVWYVVNSTYFEYLMFVLILLNTICLAMQHYGQSCLFKIAMNILNMLFTG
LFTVEMILKLIAFKPKHYFCDAWNTFDALIVVGSIVDIAITEVNPAEHTQCSPSMNAEEN
SRISITFFRLFRVMRLVKLLSRGEGIRTLLWTFIKSFQALPYVALLIVMLFFIYAVIGMQ
VFGKIALNDTTEINRNNNFQTFPQAVLLLFRCATGEAWQDIMLACMPGKKCAPESEPSNS
TEGETPCGSSFAVFYFISFYMLCAFLIINLFVAVIMDNFDYLTRDWSILGPHHLDEFKRI
WAEYDPEAKGRIKHLDVVTLLRRIQPPLGFGKLCPHRVACKRLVSMNMPLNSDGTVMFNA
TLFALVRTALRIKTEGNLEQANEELRAIIKKIWKRTSMKLLDQVVPPAGDDEVTVGKFYA
TFLIQEYFRKFKKRKEQGLVGKPSQRNA
Sequence of entity 3 (C), FASTA
>8FD7_3 Voltage-dependent L-type calcium channel subunit beta-3 (chains C)
MYEDSYVPGFEDSEAGSADSYTSRPSLDSDVSLEEDRESARREVESQAQQQLERAKHKPV
AFAVRTNVSYCGVLDEECPVQGSGINFEAKDFLHIKEKYSNDWWIGRLVKEGGDIAFIPS
PQRLESIRLKQEQKARRSGNPSSLSDIGNRRSPPPSLAKQKQKQAEHVPPYDVVPSMRPV
VLVGPSLKGYEVTDMMQKALFDFLKHRFDGRISITRVTADLSLAKRSVLNNPGKRTIIER
SSARSSIAEVQSEIERIFELAKSLQLVVLDADTINHPAQLAKTSLAPIIVFVKVSSPKVL
QRLIRSRGKSQMKHLTVQMMAYDKLVQCPPESFDVILDENQLEDACEHLAEYLEVYWRAT
HHPAPGPGLLGPPSAIPGLQSQQLLGERGEEHSPLERDSLMPSDEAWTGSSQRSSRHLEE
DYADAYQDLYQPHRQHTSGLPSANGHDPQDRLLAQDSEHNHNDRNWQRNRPWPKDSY

Ligands and cofactors

IDNameFormulaCopies
WO9(2R)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl…C34 H68 N O8 P1
CACalcium ionCa3
GBN[1-(aminomethyl)cyclohexyl]acetic acidC9 H17 N O21
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O68
CLRCholesterolC27 H46 O3
YSW(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(dodecanoyloxy)propyl…C29 H58 N O8 P1

Water and common crystallization additives (NA) are not listed.

Primary citation

Structural basis for Ca V alpha 2 delta :gabapentin binding. Chen, Z., Mondal, A., Minor Jr., D.L. Nat Struct Mol Biol (2023) 30:735-739. DOI 10.1038/s41594-023-00951-7 · PubMed

Other PDB entries of the same protein (UniProt P13806 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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