9KHC | pdb_00009khc

Crystal structure of wild-type human fibrinogen gamma chain C-terminal domain (gamma-nodule) complexed with GPRP peptide

• PDB DOI: https://doi.org/10.2210/pdb9KHC/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2024-11-10 Released: 2025-11-12 
• Deposition Author(s): Kaido, T., Kamijo, T., Arai, S., Yamauchi, K., Okumura, N., Arai, R.
• Funding Organization(s): The Japanese Society of Hematology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.169 (DCC) 

Starting Model: experimental

Literature

Crystal structure of wild-type human fibrinogen gamma chain C-terminal domain (gamma-nodule) complexed with GPRP peptide

Kaido, T., Kamijo, T., Arai, S., Yamauchi, K., Okumura, N., Arai, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.68 kDa 
• Atom Count: 4,515 
• Modeled Residue Count: 504 
• Deposited Residue Count: 554 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Gamma-A of Fibrinogen gamma chain	A, C	273	Homo sapiens	Mutation(s): 0  Gene Names: FGG, PRO2061
UniProt & NIH Common Fund Data Resources
Find proteins for P02679 (Homo sapiens) Explore P02679  Go to UniProtKB:  P02679
PHAROS:  P02679 GTEx:  ENSG00000171557

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-PRO-ARG-PRO	B, D	4	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth C], H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	E [auth A], F [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.169 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.897	α = 90
b = 66.947	β = 98.29
c = 91.428	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Kaido, T., Kamijo, T., Arai, S., Yamauchi, K., Okumura, N., Arai, R.

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Funding Organization	Location	Grant Number
The Japanese Society of Hematology	Japan	23135
Japan Society for the Promotion of Science (JSPS)	Japan	JP20K07799
Japan Society for the Promotion of Science (JSPS)	Japan	JP24K01267
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H02522
Japan Society for the Promotion of Science (JSPS)	Japan	JP17KK0104

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release