3WN5

Crystal structure of asymmetrically engineered Fc variant in complex with FcgRIIIa

PDB DOI: https://doi.org/10.2210/pdb3WN5/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2013-12-05 Released: 2014-11-19
Deposition Author(s): Kadono, S., Mimoto, F., Katada, H., Igawa, T., Kamikawa, T., Hattori, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.274
R-Value Work: 0.236
R-Value Observed: 0.238

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: 159.76 kDa
Atom Count: 9,947
Modelled Residue Count: 1,183
Deposited Residue Count: 1,314
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	A, D	230	Homo sapiens	Mutation(s): 9 Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857 Go to UniProtKB: P01857
PHAROS: P01857 GTEx: ENSG00000211896
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01857
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig gamma-1 chain C region	B, E	230	Homo sapiens	Mutation(s): 10 Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens) Explore P01857 Go to UniProtKB: P01857
PHAROS: P01857 GTEx: ENSG00000211896
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01857
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Low affinity immunoglobulin gamma Fc region receptor III-A	C, F	197	Homo sapiens	Mutation(s): 3 Gene Names: FCGR3A, CD16A, FCG3, FCGR3, IGFR3
UniProt & NIH Common Fund Data Resources
Find proteins for P08637 (Homo sapiens) Explore P08637 Go to UniProtKB: P08637
PHAROS: P08637 GTEx: ENSG00000203747
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08637
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, L	9		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain L
Glycosylation Resources
GlyTouCan: G33244HE GlyCosmos: G33244HE GlyGen: G33244HE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	5		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, M	2		N-Glycosylation	Interactions Focus chain J Focus chain M Interactions & Density Focus chain J Focus chain M
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K	8		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G59451NL GlyCosmos: G59451NL GlyGen: G59451NL

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 Z [auth F] MOL2 format, chain Z [auth F]	Z [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Z [auth F] Interactions & Density Focus chain Z [auth F]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Y [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E]	AA [auth F] BA [auth F] CA [auth F] DA [auth F] N [auth A] AA [auth F], BA [auth F], CA [auth F], DA [auth F], N [auth A], O [auth A], P [auth B], Q [auth B], R [auth B], S [auth C], T [auth C], U [auth D], V [auth E], W [auth E], X [auth E], Y [auth E]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.274
R-Value Work: 0.236
R-Value Observed: 0.238
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.03	α = 90
b = 72.49	β = 91.15
c = 163.48	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-11-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-19
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary