9L6Q | pdb_00009l6q

Vitamin K-dependent gamma-carboxylase in complex with Coagulation factor IX and vitamin K

PDB DOI: https://doi.org/10.2210/pdb9L6Q/pdb
EM Map EMD-62862: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-12-25 Released: 2025-10-08
Deposition Author(s): Hang, J., Chen, D.D., Zhong, Q.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.78 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Molecular basis of vitamin K-dependent protein gamma-glutamyl carboxylation.

Zhong, Q., Chen, D., Xu, J., Li, Y., Yuan, W., Meng, Y., Wen, Q., Ye, Q., Wang, G., Pan, K., Song, C., Tao, L., Qiao, J., Hang, J.

(2025) Cell Res 35: 917-920

PubMed: 41016932 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-025-01185-6
Primary Citation Related Structures:
9L6Q, 9L6R, 9L6S

Organizational Affiliation

State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.

National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Key Laboratory of Assisted Reproduction, Ministry of Education (Peking University), Beijing key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, China.

Department of Biophysics, School of Basic Medical Sciences, Peking University, Beijing, China.

School of Basic Medical Sciences, Peking University, Beijing, China.

Beijing Academy of Artificial Intelligence, Beijing, China.

School of Life Sciences, Tsinghua University, Beijing, China.

Department of Orthopedics, Engineering Research Center of Bone and Joint Precision Medicine, Ministry of Education, Beijing Key Laboratory of Spinal Disease Research, Peking University Third Hospital, Beijing, China.

State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China.

Department of Orthopedics, First Hospital of China Medical University, Shenyang, Liaoning, China.

Department of Orthopedics, First Hospital of China Medical University, Shenyang, Liaoning, China. taolindr@163.com.

State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China. jie.qiao@263.net.

State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China. hangjbysy@bjmu.edu.cn.

Institute of Advanced Clinical Medicine, Peking University, Beijing, China. hangjbysy@bjmu.edu.cn.

Macromolecule Content

Total Structure Weight: 143.28 kDa
Atom Count: 5,853
Modeled Residue Count: 697
Deposited Residue Count: 1,219
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin K-dependent gamma-carboxylase	A	758	Homo sapiens	Mutation(s): 0 Gene Names: GGCX, GC EC: 4.1.1.90
UniProt & NIH Common Fund Data Resources
Find proteins for P38435 (Homo sapiens) Explore P38435 Go to UniProtKB: P38435
PHAROS: P38435 GTEx: ENSG00000115486
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38435
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: P38435-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	B [auth C]	461	Homo sapiens	Mutation(s): 0 Gene Names: F9 EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens) Explore P00740 Go to UniProtKB: P00740
PHAROS: P00740 GTEx: ENSG00000101981
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00740
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B], D	2		N-Glycosylation	Interactions Focus chain C [auth B] Focus chain D Interactions & Density Focus chain C [auth B] Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6PL (Subject of Investigation/LOI) Query on 6PL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE C₄₂ H₈₅ N O₈ P PZNPLUBHRSSFHT-RRHRGVEJSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
1L3 (Subject of Investigation/LOI) Query on 1L3 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	Menaquinone-4 C₃₁ H₄₀ O₂ DKHGMERMDICWDU-GHDNBGIDSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CLR (Subject of Investigation/LOI) Query on CLR Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]