6FGO

Fc in complex with engineered calcium binding domain Z

PDB DOI: https://doi.org/10.2210/pdb6FGO/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Staphylococcus aureus
Expression System: Cricetulus griseus, Escherichia coli
Mutation(s): No

Deposited: 2018-01-11 Released: 2018-06-20
Deposition Author(s): Venskutonyte, R., Kanje, S., Hober, S., Lindkvist-Petersson, K.
Funding Organization(s): Vinnova

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.232
R-Value Work: 0.203
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 133.43 kDa
Atom Count: 9,382
Modelled Residue Count: 1,094
Deposited Residue Count: 1,116
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin gamma-1 heavy chain	A, C [auth B], E [auth C], G [auth D]	210	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5 Go to UniProtKB: P0DOX5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DOX5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Z-Ca	B [auth E], D [auth F], F [auth G], H	69	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for A0A0U3TLJ6 (Staphylococcus aureus) Explore A0A0U3TLJ6 Go to UniProtKB: A0A0U3TLJ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0U3TLJ6
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-(1-2)-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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I, K	8		N-Glycosylation	Interactions Focus chain I Focus chain K Interactions & Density Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G80858MF GlyCosmos: G80858MF GlyGen: G80858MF

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	J	7		N-Glycosylation	Interactions Focus chain J Interactions & Density Focus chain J
Glycosylation Resources
GlyTouCan: G45889JQ GlyCosmos: G45889JQ GlyGen: G45889JQ

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	L	5		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A]	HA [auth C], IA [auth C], JA [auth C], M [auth A], N [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain M [auth A] Focus chain N [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain S [auth E] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	AA [auth F] BA [auth F] KA [auth C] LA [auth C] MA [auth C] AA [auth F], BA [auth F], KA [auth C], LA [auth C], MA [auth C], O [auth A], P [auth A], Q [auth A], QA [auth D], RA [auth D], S [auth E], V [auth B], W [auth B], X [auth B], Y [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth E] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth E] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain NA [auth G] SDF format, chain R [auth E] SDF format, chain SA [auth H] SDF format, chain Z [auth F] MOL2 format, chain NA [auth G] MOL2 format, chain R [auth E] MOL2 format, chain SA [auth H] MOL2 format, chain Z [auth F]	NA [auth G], R [auth E], SA [auth H], Z [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain NA [auth G] Focus chain R [auth E] Focus chain SA [auth H] Focus chain Z [auth F] Interactions & Density Focus chain NA [auth G] Focus chain R [auth E] Focus chain SA [auth H] Focus chain Z [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] GA [auth C] CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], OA [auth D], PA [auth D], T [auth B], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain T [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.232
R-Value Work: 0.203
R-Value Observed: 0.205
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.229	α = 90
b = 120.296	β = 90
c = 126.33	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-06-20

Deposition Author(s):

Venskutonyte, R.

Kanje, S.

Hober, S.

Lindkvist-Petersson, K.

Funding Organization	Location	Grant Number
Vinnova	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2018-06-20
Type: Initial release
Version 1.1: 2018-08-29
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary