9L6Q: Vitamin K-dependent gamma-carboxylase

Vitamin K-dependent gamma-carboxylase in complex with Coagulation factor IX and vitamin K. Determined by electron microscopy at 2.78 Å resolution. Released 8 Oct 2025.

Method: Electron microscopy
Resolution: 2.78 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,853
Mol. weight: 143.28 kDa
Ligands: 1L3, CLR, 6PL
Released: 8 Oct 2025

Explore 9L6Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L6Q contains 43 α-helices and 23 β-strands across 2 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 A: 41 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	33-38	6
α-helix	42-45	4
α-helix	48-55	8
β-strand	58-59	2	1
α-helix	62-78	17
α-helix	79-83	5
α-helix	85-87	3
α-helix	88-91	4
β-strand	99	1	2
α-helix	109-111	3
α-helix	112-131	20
α-helix	135-152	18
α-helix	154-156	3
α-helix	159-173	15
α-helix	182-186	5
β-strand	193	1	3
β-strand	195-196	2	1
α-helix	197-218	22
α-helix	221-224	4
α-helix	236-238	3
α-helix	239-244	6
α-helix	247-249	3
α-helix	250-258	9
α-helix	259-271	13
α-helix	276-293	18
α-helix	299-306	8
α-helix	307-309	3
α-helix	315-322	8
α-helix	336-337	2
β-strand	338	1	3
α-helix	339	1
α-helix	358-376	19
α-helix	377-379	3
α-helix	385-387	3
β-strand	406-416	11	4
β-strand	423-426	4	4
β-strand	432	1	2
α-helix	436-439	4
α-helix	441-454	14
α-helix	455-458	4
β-strand	464-473	10	4
β-strand	478	1	5
β-strand	479-480	2	4
β-strand	482	1	6
α-helix	488-490	3
β-strand	502	1	6
α-helix	503-505	3
α-helix	507-509	3
α-helix	512-522	11
β-strand	528-534	7	5
β-strand	539-543	5	7
β-strand	551-557	7	5
β-strand	560-564	5	7
β-strand	569-573	5	7
α-helix	574	1
β-strand	578-581	4	5
β-strand	586-591	6	7
β-strand	597-603	7	5
α-helix	606-624	19
α-helix	654-674	21
α-helix	677-707	31
α-helix	713-723	11

Chain C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	4
α-helix	34-37	4
α-helix	43-44	2
β-strand	50	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin K-dependent gamma-carboxylase	A	protein	758	Homo sapiens	P38435 (AlphaFold model)
Coagulation factor IX	C	protein	461	Homo sapiens	P00740 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9L6Q_1 Vitamin K-dependent gamma-carboxylase (chains A)
MAVSAGSARTSPSSDKVQKDKAELISGPRQDSRIGKLLGFEWTDLSSWRRLVTLLNRPTD
PASLAVFRFLFGFLMVLDIPQERGLSSLDRKYLDGLDVCRFPLLDALRPLPLDWMYLVYT
IMFLGALGMMLGLCYRISCVLFLLPYWYVFLLDKTSWNNHSYLYGLLAFQLTFMDANHYW
SVDGLLNAHRRNAHVPLWNYAVLRGQIFIVYFIAGVKKLDADWVEGYSMEYLSRHWLFSP
FKLLLSEELTSLLVVHWGGLLLDLSAGFLLFFDVSRSIGLFFVSYFHCMNSQLFSIGMFS
YVMLASSPLFCSPEWPRKLVSYCPRRLQQLLPLKAAPQPSVSCVYKRSRGKSGQKPGLRH
QLGAAFTLLYLLEQLFLPYSHFLTQGYNNWTNGLYGYSWDMMVHSRSHQHVKITYRDGRT
GELGYLNPGVFTQSRRWKDHADMLKQYATCLSRLLPKYNVTEPQIYFDIWVSINDRFQQR
IFDPRVDIVQAAWSPFQRTSWVQPLLMDLSPWRAKLQEIKSSLDNHTEVVFIADFPGLHL
ENFVSEDLGNTSIQLLQGEVTVELVAEQKNQTLREGEKMQLPAGEYHKVYTTSPSPSCYM
YVYVNTTELALEQDLAYLQELKEKVENGSETGPLPPELQPLLEGEVKGGPEPTPLVQTFL
RRQQRLQEIERRRNTPFHERFFRFLLRKLYVFRRSFLMTCISLRNLILGRPSLEQLAQEV
TYANLRPFEAVGELNPSNTDSSHSNPPESNPDPVHSEF

Sequence of entity 2 (C), FASTA

>9L6Q_2 Coagulation factor IX (chains C)
MQRVNMIMAESPGLITICLLGYLLSAECTVFLDHENANKILNRPKRYNSGKLEEFVQGNL
ERECMEEKCSFEEAREVFENTERTTEFWKQYVDGDQCESNPCLNGGSCKDDINSYECWCP
FGFEGKNCELDVTCNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGR
VSVSQTSKLTRAETVFPDVDYVNSTEAETILDNITQSTQSFNDFTRVVGGEDAKPGQFPW
QVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRII
PHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVF
HKGRSALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVE
GTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT

Ligands and cofactors

ID	Name	Formula	Copies
1L3	Menaquinone-4	C31 H40 O2	1
CLR	Cholesterol	C27 H46 O	1
6PL	(4S,7R)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4…	C42 H85 N O8 P	2

Primary citation

Molecular basis of vitamin K-dependent protein gamma-glutamyl carboxylation. Zhong, Q., Chen, D., Xu, J. et al. Cell Res (2025) 35:917-920. DOI 10.1038/s41422-025-01185-6 · PubMed

Other PDB entries of the same protein (UniProt P38435 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9L25 2.41 Å, cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX(Gla)
9L6S 2.58 Å, double-mutant (K217A & K218A) Vitamin K-dependent gamma-carboxylase in complex with…
9L6R 2.59 Å, double-mutant (K217A & K218A) Vitamin K-dependent gamma-carboxylase in complex with…
9L21 2.62 Å, cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX
9L23 2.62 Å, cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with Osteocalcin
9WF3 2.65 Å, Cryo-EM structure of GGCX-FIX complex
13IB 2.68 Å, Structure of GGCX-BGP-Anisindione complex
9WFL 2.75 Å, Cryo-EM structure of GGCX-PRGP1 complex
9L20 2.82 Å, cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with anisindione
9WF9 2.83 Å, Cryo-EM structure of GGCX-FX complex
9WF2 2.94 Å, Cryo-EM structure of GGCX-BGP complex
9WFN 2.94 Å, Cryo-EM structure of GGCX-proP2

Browse structure collections

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