6QF7

Crystal structures of the recombinant beta-Factor XIIa protease with bound Thr-Arg and Pro-Arg substrate mimetics

PDB DOI: https://doi.org/10.2210/pdb6QF7/pdb

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

Deposited: 2019-01-09 Released: 2019-06-05
Deposition Author(s): Pathak, M., Mannal, R., Li, C., Bubacarr, G.K., Badraldin, K.H., Belviso, B.D., Camila, R.B., Dreveny, I., Fischer, P.M., Dekker, L.V., Oliva, M.L.V., Emsley, J.
Funding Organization(s): British Heart Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.356
R-Value Work: 0.297
R-Value Observed: 0.303

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 137.71 kDa
Atom Count: 9,512
Modelled Residue Count: 1,227
Deposited Residue Count: 1,256
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein	A, C	374	Escherichia coli	Mutation(s): 0 Gene Names: malE, NCTC8450_00456, NCTC9775_03059
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XII	B, D	254	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00748
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	E	2		N/A	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	F, G	2		N/A	Interactions Focus chain F Focus chain G Interactions & Density Focus chain F Focus chain G
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0G6 Query on 0G6 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth D] MOL2 format, chain I [auth B] MOL2 format, chain J [auth D]	I [auth B], J [auth D]	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide C₂₁ H₃₄ Cl N₆ O₃ DVFLYEYCMMLBTQ-VSZNYVQBSA-O		Interactions Focus chain I [auth B] Focus chain J [auth D] Interactions & Density Focus chain I [auth B] Focus chain J [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 6
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000020 (0G6) Query on PRD_000020	I [auth B], J [auth D]	D-Phe-Pro-Arg-CH2Cl	Peptide-like / Inhibitor		Interactions Focus chain I [auth B] Focus chain J [auth D] Interactions & Density Focus chain I [auth B] Focus chain J [auth D]

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	F, G	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain F Focus chain G Interactions & Density Focus chain F Focus chain G

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.356
R-Value Work: 0.297
R-Value Observed: 0.303
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.45	α = 90
b = 131.45	β = 90
c = 238.35	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-06-05

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: 2019-06-05
Type: Initial release
Version 1.1: 2019-06-26
Changes: Data collection, Database references
Version 1.2: 2019-07-31
Changes: Data collection, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary