9L6S: Coagulation factor X

double-mutant (K217A & K218A) Vitamin K-dependent gamma-carboxylase in complex with coagulation factors X and vitamin K. Determined by electron microscopy at 2.58 Å resolution. Released 8 Oct 2025.

Method: Electron microscopy
Resolution: 2.58 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,834
Mol. weight: 146.52 kDa
Ligands: NAG, A1EMC, 6PL, CLR
Released: 8 Oct 2025

Explore 9L6S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L6S contains 42 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: 41 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	59	1	2
α-helix	62-78	17
α-helix	85-87	3
α-helix	88-91	4
α-helix	109-111	3
α-helix	112-131	20
α-helix	135-151	17
α-helix	154-156	3
α-helix	159-171	13
α-helix	182-186	5
α-helix	188-190	3
β-strand	193	1	3
β-strand	195	1	2
α-helix	197-217	21
α-helix	221-224	4
α-helix	232-234	3
α-helix	236-238	3
α-helix	241-243	3
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	315-321	7
α-helix	325-328	4
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	1
β-strand	423-426	4	1
α-helix	436-438	3
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	507-512	6
α-helix	513-521	9
β-strand	527-534	8	4
β-strand	539-543	5	6
β-strand	551-557	7	4
β-strand	560-564	5	6
β-strand	569-572	4	6
β-strand	578-581	4	4
β-strand	586-591	6	6
β-strand	597-604	8	4
α-helix	606-627	22
α-helix	654-673	20
α-helix	677-707	31
α-helix	713-723	11

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	25-26	2	1
α-helix	28-31	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor X	C	protein	488	Homo sapiens	P00742 (AlphaFold model)
Vitamin K-dependent gamma-carboxylase	A	protein	758	Homo sapiens	P38435 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9L6S_1 Coagulation factor X (chains C)
MGRPLHLVLLSASLAGLLLLGESLFIRREQANNILARVTRANSFLEEMKKGHLERECMEE
TCSYEEAREVFEDSDKTNEFWNKYKDGDQCETSPCQNQGKCKDGLGEYTCTCLEGFEGKN
CELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLERR
KRSVAQATSSSGEAPDSITWKPYDAADLDPTENPFDLLDFNQTQPERGDNNLTRIVGGQE
CKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGE
AVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGI
VSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSG
GPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLPKAKSHAPE
VITSSPLK

Sequence of entity 2 (A), FASTA

>9L6S_2 Vitamin K-dependent gamma-carboxylase (chains A)
MAVSAGSARTSPSSDKVQKDKAELISGPRQDSRIGKLLGFEWTDLSSWRRLVTLLNRPTD
PASLAVFRFLFGFLMVLDIPQERGLSSLDRKYLDGLDVCRFPLLDALRPLPLDWMYLVYT
IMFLGALGMMLGLCYRISCVLFLLPYWYVFLLDKTSWNNHSYLYGLLAFQLTFMDANHYW
SVDGLLNAHRRNAHVPLWNYAVLRGQIFIVYFIAGVAALDADWVEGYSMEYLSRHWLFSP
FKLLLSEELTSLLVVHWGGLLLDLSAGFLLFFDVSRSIGLFFVSYFHCMNSQLFSIGMFS
YVMLASSPLFCSPEWPRKLVSYCPRRLQQLLPLKAAPQPSVSCVYKRSRGKSGQKPGLRH
QLGAAFTLLYLLEQLFLPYSHFLTQGYNNWTNGLYGYSWDMMVHSRSHQHVKITYRDGRT
GELGYLNPGVFTQSRRWKDHADMLKQYATCLSRLLPKYNVTEPQIYFDIWVSINDRFQQR
IFDPRVDIVQAAWSPFQRTSWVQPLLMDLSPWRAKLQEIKSSLDNHTEVVFIADFPGLHL
ENFVSEDLGNTSIQLLQGEVTVELVAEQKNQTLREGEKMQLPAGEYHKVYTTSPSPSCYM
YVYVNTTELALEQDLAYLQELKEKVENGSETGPLPPELQPLLEGEVKGGPEPTPLVQTFL
RRQQRLQEIERRRNTPFHERFFRFLLRKLYVFRRSFLMTCISLRNLILGRPSLEQLAQEV
TYANLRPFEAVGELNPSNTDSSHSNPPESNPDPVHSEF

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
A1EMC	2-methyl-3-[(2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetrae…	C31 H42 O2	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
CLR	Cholesterol	C27 H46 O	1

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 P00742 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9I24 1.2 Å, Coagulation factor Xa complex with a2-loop peptide
2JKH 1.25 Å, Factor Xa - cation inhibitor complex
2Y5F 1.29 Å, Factor xa - cation inhibitor complex
2Y5G 1.29 Å, Factor xa - cation inhibitor complex
2Y5H 1.33 Å, Factor xa - cation inhibitor complex
3KL6 1.45 Å, Discovery of Tetrahydropyrimidin-2(1H)-one derivative TAK-442: A potent, selective and…
2PR3 1.5 Å, Factor XA inhibitor
6YYX 1.53 Å, Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with…
3FFG 1.54 Å, Factor XA in complex with the inhibitor (R)-6-(2'-((3- HYDROXYPYRROLIDIN-1-YL)METHYL)BIPH…
7YB9 1.54 Å, Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with…
4Y6D 1.55 Å, Factor Xa complex with GTC000101
2VWO 1.6 Å, Aminopyrrolidine Factor Xa inhibitor

Browse structure collections

About this viewer

MolViewer shows 9L6S directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.