9WFN: GGCX-proP2

Cryo-EM structure of GGCX-proP2. Determined by electron microscopy at 2.94 Å resolution. Released 1 Apr 2026.

Method: Electron microscopy
Resolution: 2.94 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,701
Mol. weight: 87.8 kDa
Ligands: NAG, POV, MX7, CLR
Released: 1 Apr 2026

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

Secondary structure: helices and β-sheets

9WFN contains 45 α-helices and 20 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: 44 helices, 19 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	2
α-helix	62-81	20
α-helix	85-87	3
α-helix	88-91	4
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	176-178	3
α-helix	182-186	5
β-strand	193	1	3
β-strand	195-196	2	2
α-helix	197-217	21
α-helix	221-224	4
α-helix	230-234	5
α-helix	236-238	3
α-helix	239-242	4
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	307-310	4
α-helix	315-322	8
α-helix	325-330	6
α-helix	336-337	2
β-strand	338	1	3
α-helix	339	1
α-helix	355-357	3
α-helix	358-376	19
α-helix	377-382	6
α-helix	385-387	3
β-strand	406-416	11	1
β-strand	423-426	4	1
α-helix	436-439	4
α-helix	441-454	14
α-helix	455-458	4
β-strand	464-473	10	1
β-strand	478	1	4
β-strand	479-480	2	1
β-strand	482	1	5
β-strand	502	1	5
α-helix	503-505	3
α-helix	507-509	3
α-helix	510-521	12
β-strand	527-534	8	4
β-strand	539-543	5	6
β-strand	548-557	10	4
β-strand	560-564	5	6
β-strand	569-573	5	6
α-helix	574	1
β-strand	578-580	3	4
β-strand	586-591	6	6
α-helix	596	1
β-strand	597-605	9	4
α-helix	606-617	12
α-helix	657-674	18
α-helix	677-708	32
α-helix	713-724	12

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	31-32	2	1
α-helix	36-38	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor IX	B	protein	16	Homo sapiens	P00740 (AlphaFold model)
Vitamin K-dependent gamma-carboxylase	A	protein	696	Homo sapiens	P38435 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9WFN_1 Coagulation factor IX (chains B)
TVFLDHENANKILNRP

Sequence of entity 2 (A), FASTA

>9WFN_2 Vitamin K-dependent gamma-carboxylase (chains A)
SRIGKLLGFEWTDLSSWRRLVTLLNRPTDPASLAVFRFLFGFLMVLDIPQERGLSSLDRK
YLDGLDVCRFPLLDALRPLPLDWMYLVYTIMFLGALGMMLGLCYRISCVLFLLPYWYVFL
LDKTSWNNHSYLYGLLAFQLTFMDANHYWSVDGLLNAHRRNAHVPLWNYAVLRGQIFIVY
FIAGVKKLDADWVEGYSMEYLSRHWLFSPFKLLLSEELTSLLVVHWGGLLLDLSAGFLLF
FDVSRSIGLFFVSYFHCMNSQLFSIGMFSYVMLASSPLFCSPEWPRKLVSYCPRRLQQLL
PLKAAPQPSVSCVYKRSRGKSGQKPGLRHQLGAAFTLLYLLEQLFLPYSHFLTQGYNNWT
NGLYGYSWDMMVHSRSHQHVKITYRDGRTGELGYLNPGVFTQSRRWKDHADMLKQYATCL
SRLLPKYNVTEPQIYFDIWVSINDRFQQRIFDPRVDIVQAAWSPFQRTSWVQPLLMDLSP
WRAKLQEIKSSLDNHTEVVFIADFPGLHLENFVSEDLGNTSIQLLQGEVTVELVAEQKNQ
TLREGEKMQLPAGEYHKVYTTSPSPSCYMYVYVNTTELALEQDLAYLQELKEKVENGSET
GPLPPELQPLLEGEVKGGPEPTPLVQTFLRRQQRLQEIERRRNTPFHERFFRFLLRKLYV
FRRSFLMTCISLRNLILGRPSLEQLAQEVTYANLRP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	2
MX7	(2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate	C39 H73 O8 P	1
CLR	Cholesterol	C27 H46 O	1
A1AT1	(1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tet…	C31 H40 O3	1

Primary citation

Cryo-EM structure of GGCX-proP2 complex. Qian, H.W., Chen, Q.Y. To be published.

Other PDB entries of the same protein (UniProt P00740 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JB9 1.3 Å, Crystal structure of factor IXa K98T variant in complex with PPACK
6MV4 1.37 Å, Crystal structure of human coagulation factor ixa
5JBA 1.4 Å, Crystal structure of factor IXa variant V16I K98T Y177T I212V in complex with PPACK
5TNT 1.4 Å, Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa…
4YZU 1.41 Å, Rapid development of two Factor IXa inhibitors from Hit to Lead
4Z0K 1.41 Å, Rapid development of two Factor IXa inhibitors from Hit to Lead
5JB8 1.45 Å, Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone
1EDM 1.5 Å, Epidermal growth factor-like domain from human factor IX
2WPH 1.5 Å, factor IXa superactive triple mutant
5TNO 1.54 Å, Discovery of novel aminobenzisoxazole derivatives as orally available factor IXa…
5JBB 1.56 Å, Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with…
2WPJ 1.6 Å, factor IXa superactive triple mutant, NaCl-soaked

Browse structure collections

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