7PRK | pdb_00007prk

Factor XII Fibronectin type II (FXII FnII) domain

PDB DOI: https://doi.org/10.2210/pdb7PRK/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2021-09-21 Released: 2022-10-05
Deposition Author(s): Kaira, B.G., Emsley, J.
Funding Organization(s): British Heart Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.204 (Depositor), 0.218 (DCC)
R-Value Work:
0.170 (Depositor), 0.182 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Factor XII Fibronectin type II (FXII FnII) domain

Kaira, B.G., Emsley, J.

To be published.

Macromolecule Content

Total Structure Weight: 8.57 kDa
Atom Count: 496
Modeled Residue Count: 54
Deposited Residue Count: 71
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XII	A	71	Homo sapiens	Mutation(s): 0 Gene Names: F12 EC: 3.4.21.38
UniProt & NIH Common Fund Data Resources
Find proteins for P00748 (Homo sapiens) Explore P00748 Go to UniProtKB: P00748
PHAROS: P00748 GTEx: ENSG00000131187
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00748
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.204 (Depositor), 0.218 (DCC)
R-Value Work: 0.170 (Depositor), 0.182 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.82	α = 90
b = 45.82	β = 90
c = 53.5	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-10-05

Deposition Author(s):

Funding Organization	Location	Grant Number
British Heart Foundation	United Kingdom	RG/12/9/29775

Revision History (Full details and data files)

Version 1.0: 2022-10-05
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.