6YAX | pdb_00006yax

Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05)

PDB DOI: https://doi.org/10.2210/pdb6YAX/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-03-14 Released: 2021-10-06
Deposition Author(s): Fisher, H., Tews, I., Orr, C.
Funding Organization(s): Cancer Research UK

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.264 (Depositor), 0.270 (DCC)
R-Value Work:
0.230 (Depositor), 0.230 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of CD32b (Fc Gamma Receptor IIb) in complex with Human IgG1 Fab fragment (5C05)

Fisher, H., Tews, I., Orr, C.

To be published.

Macromolecule Content

Total Structure Weight: 134.42 kDa
Atom Count: 8,665
Modeled Residue Count: 1,096
Deposited Residue Count: 1,234
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5C05 F(ab) heavy chain	A [auth HHH], E [auth III]	218	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5C05 F(ab) light chain	B [auth MMM], D [auth LLL]	218	Homo sapiens	Mutation(s): 0
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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Low affinity immunoglobulin gamma Fc region receptor II-c	C [auth AAA], F [auth BBB]	181	Homo sapiens	Mutation(s): 0 Gene Names: FCGR2C, CD32, FCG2, IGFR2
UniProt & NIH Common Fund Data Resources
Find proteins for P31995 (Homo sapiens) Explore P31995 Go to UniProtKB: P31995
PHAROS: P31995
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31995
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth AAA] Focus chain F [auth BBB]	Go to GlyGen: P31995-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth A]	2		N-Glycosylation	Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth AAA] MOL2 format, chain I [auth AAA] mmCIF format, chain I [auth AAA]	I [auth AAA]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth AAA] Interactions & Density Focus chain I [auth AAA]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain H [auth HHH] SDF format, chain K [auth III] MOL2 format, chain H [auth HHH] MOL2 format, chain K [auth III] mmCIF format, chain H [auth HHH] mmCIF format, chain K [auth III]	H [auth HHH], K [auth III]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain H [auth HHH] Focus chain K [auth III] Interactions & Density Focus chain H [auth HHH] Focus chain K [auth III]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth LLL] MOL2 format, chain J [auth LLL] mmCIF format, chain J [auth LLL]	J [auth LLL]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth LLL] Interactions & Density Focus chain J [auth LLL]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.264 (Depositor), 0.270 (DCC)
R-Value Work: 0.230 (Depositor), 0.230 (DCC)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.728	α = 90
b = 95.728	β = 90
c = 186.038	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

Fisher, H.

Tews, I.

Orr, C.

Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	S_3591

Revision History (Full details and data files)

Version 1.0: 2021-10-06
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary