1FE8

CRYSTAL STRUCTURE OF THE VON WILLEBRAND FACTOR A3 DOMAIN IN COMPLEX WITH A FAB FRAGMENT OF IGG RU5 THAT INHIBITS COLLAGEN BINDING

PDB DOI: https://doi.org/10.2210/pdb1FE8/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2000-07-21 Released: 2001-04-04
Deposition Author(s): Bouma, B., Huizinga, E.G., Schiphorst, M.E., Sixma, J.J., Kroon, J., Gros, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.264
R-Value Work: 0.227
R-Value Observed: 0.229

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: 201.59 kDa
Atom Count: 14,872
Modelled Residue Count: 1,834
Deposited Residue Count: 1,851
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VON WILLEBRAND FACTOR	A, D [auth B], G [auth C]	196	Homo sapiens	Mutation(s): 4
UniProt & NIH Common Fund Data Resources
Find proteins for P04275 (Homo sapiens) Explore P04275 Go to UniProtKB: P04275
PHAROS: P04275 GTEx: ENSG00000110799
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04275
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN IGG RU5	B [auth H], E [auth I], H [auth J]	210	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01863 (Mus musculus) Explore P01863 Go to UniProtKB: P01863
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01863
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN IGG RU5	C [auth L], F [auth M], I [auth N]	211	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth D], K [auth E], L [auth F]	2		N-Glycosylation	Interactions Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth H] SDF format, chain O [auth I] MOL2 format, chain M [auth H] MOL2 format, chain O [auth I]	M [auth H], O [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth H] Focus chain O [auth I] Interactions & Density Focus chain M [auth H] Focus chain O [auth I]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain N [auth L] MOL2 format, chain N [auth L]	N [auth L]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain N [auth L] Interactions & Density Focus chain N [auth L]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, D [auth B], G [auth C]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
RU5	PDBBind: 1FE8	Kd: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.264
R-Value Work: 0.227
R-Value Observed: 0.229
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.8	α = 90
b = 183.6	β = 116.2
c = 131.8	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2001-04-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-04-04
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary