9WF3 | pdb_00009wf3

Cryo-EM structure of GGCX-FIX complex

PDB DOI: https://doi.org/10.2210/pdb9WF3/pdb
EM Map EMD-65922: EMDB EMDataResource

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

Deposited: 2025-08-21 Released: 2026-04-01
Deposition Author(s): Qian, H.W., Zhang, W.J.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.65 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of GGCX-FIX complex

Qian, H.W., Zhang, W.J.

To be published.

Macromolecule Content

Total Structure Weight: 89.4 kDa
Atom Count: 5,781
Modeled Residue Count: 680
Deposited Residue Count: 725
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin K-dependent gamma-carboxylase	A	697	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38435
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A	Go to GlyGen: P38435-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	B	28	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00740
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Interactions & Density Focus chain C Focus chain D Focus chain E

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A]	G [auth A], I [auth A]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain I [auth A]
MX7 Query on MX7 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]	(2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate C₃₉ H₇₃ O₈ P MHUWZNTUIIFHAS-DSSVUWSHSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
A1AT1 (Subject of Investigation/LOI) Query on A1AT1 Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	(1aR,7aS)-1a-methyl-7a-[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]-1a,7a-dihydronaphtho[2,3-b]oxirene-2,7-dione C₃₁ H₄₀ O₃ TUZHANAISKEZFG-YNKDMHFFSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth A]	F [auth A], K [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain K [auth A] Interactions & Density Focus chain F [auth A] Focus chain K [auth A]