13IB: GGCX-BGP-Anisindione complex

Structure of GGCX-BGP-Anisindione complex. Determined by electron microscopy at 2.68 Å resolution. Released 2 Sept 2026.

Method: Electron microscopy
Resolution: 2.68 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,027
Mol. weight: 100.9 kDa
Ligands: NAG, CLR, A1AT0, POV
Released: 2 Sept 2026

Explore 13IB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

13IB contains 42 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	35-38	4
α-helix	42-45	4
α-helix	48-55	8
β-strand	58-59	2	1
α-helix	62-78	17
α-helix	88-91	4
β-strand	99	1	2
α-helix	109-111	3
α-helix	112-131	20
α-helix	135-151	17
α-helix	154-156	3
α-helix	159-172	14
α-helix	182-186	5
α-helix	188-190	3
β-strand	193	1	3
β-strand	195-196	2	1
α-helix	198-217	20
α-helix	221-224	4
α-helix	230-234	5
α-helix	236-238	3
α-helix	239-242	4
α-helix	247-250	4
α-helix	251-258	8
α-helix	259-271	13
α-helix	276-293	18
α-helix	299-306	8
α-helix	307-310	4
α-helix	315-320	6
α-helix	326-329	4
α-helix	332-333	2
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	436-438	3
α-helix	441-454	14
α-helix	455-458	4
β-strand	466-473	8	4
β-strand	478	1	5
β-strand	479-480	2	4
β-strand	482	1	6
β-strand	502	1	6
α-helix	503-505	3
α-helix	507-509	3
α-helix	513-521	9
β-strand	527-534	8	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
β-strand	578-581	4	5
β-strand	586-591	6	7
β-strand	597-604	8	5
α-helix	606-622	17
α-helix	654-673	20
α-helix	677-708	32
α-helix	713-723	11

Chain B: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	36-37	2	4
β-strand	65	1	4
α-helix	89-95	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin K-dependent gamma-carboxylase	A	protein	758	Homo sapiens	P38435 (AlphaFold model)
Osteocalcin	B	protein	100	Homo sapiens	P02818 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>13IB_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 (B), FASTA

>13IB_2 Osteocalcin (chains B)
MRALTLLALLALAALCIAGQAGAKPSGAESSKGAAFVSKQEGSEVVKRPRRYLYQWLGAP
VPYPDPLEPRREVCELNPDCDELADHIGFQEAYRRFYGPV

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
CLR	Cholesterol	C27 H46 O	1
A1AT0	anisindione	C16 H12 O3	1
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	1

Primary citation

gamma-glutamyl carboxylase inhibition by Anisindione. Zhou, N., Wang, R., Chen, B. et al. Structure (2026). DOI 10.1016/j.str.2026.08.002 · 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
9WFL 2.75 Å, Cryo-EM structure of GGCX-PRGP1 complex
9L6Q 2.78 Å, Vitamin K-dependent gamma-carboxylase in complex with Coagulation factor IX and vitamin K
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

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