6B74

Structures of the two-chain human plasma Factor XIIa co-crystallized with potent inhibitors

PDB DOI: https://doi.org/10.2210/pdb6B74/pdb

Classification: BLOOD CLOTTING
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2017-10-03 Released: 2018-03-21
Deposition Author(s): Dementiev, A.A., Partridge, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.222
R-Value Work: 0.190
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 28.33 kDa
Atom Count: 1,952
Modelled Residue Count: 252
Deposited Residue Count: 252
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor XII	A	9	Homo sapiens	Mutation(s): 0 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
UniProt Group	P00748
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	243	Homo sapiens	Mutation(s): 0 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	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B]	E [auth B], F [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B]
BEN Query on BEN Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B]	D [auth B]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B]	G [auth B], H [auth B], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.222
R-Value Work: 0.190
R-Value Observed: 0.193
Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.289	α = 90
b = 80.289	β = 90
c = 121.731	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Dementiev, A.A.

Partridge, J.R.

Revision History (Full details and data files)

Version 1.0: 2018-03-21
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

6B74

Structures of the two-chain human plasma Factor XIIa co-crystallized with potent inhibitors

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2