6RFK | pdb_00006rfk

Crystal structure of EGRCK-inhibited Gla-domainless fIXa (K148Q, R150Q variant)

• PDB DOI: https://doi.org/10.2210/pdb6RFK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-04-15 Released: 2019-06-12 
• Deposition Author(s): Huntington, J.A., Sendall, T.J.
• Funding Organization(s): British Heart Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.163 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Starting Model: experimental

Literature

NMR resonance assignments of apo and EGRCK-inhibited factor IXa

Sendall, T.J., Huntington, J.A.

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)

Macromolecule Content 

• Total Structure Weight: 34.64 kDa 
• Atom Count: 2,625 
• Modeled Residue Count: 301 
• Deposited Residue Count: 301 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	A [auth E]	62	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	B [auth S]	235	Homo sapiens	Mutation(s): 2  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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GLU-GLY-AR7-0QE	C [auth I]	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3P	D [auth E]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
GOL	F [auth S], G [auth S], H [auth S], I [auth S], J [auth S], K [auth S], L [auth S], M [auth S], N [auth S], O [auth S]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth S]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AR7	C [auth I]	PEPTIDE-LIKE	C6 H17 N4 O2		ARG

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000288 (0GJ)	C [auth I]	GLU-GLY-ARG-CHLOROMETHYL KETONE	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.163 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.16	α = 90
b = 100.16	β = 90
c = 91.5	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Huntington, J.A., Sendall, T.J.

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Funding Organization	Location	Grant Number
British Heart Foundation	United Kingdom	PG/11/91/29117

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2019-07-31
  Changes: Data collection, Structure summary
• Version 1.2: 2024-01-24
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary