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 
- 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. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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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 AnnotationsExpand | |||||
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Find similar proteins by:
(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 AnnotationsExpand | |||||
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Oligosaccharides
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 | ||
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 | ||
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 | ||
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 | HA [auth C], IA [auth C], JA [auth C], M [auth A], N [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
GOL Query on GOL | AA [auth F] BA [auth F] KA [auth C] LA [auth C] MA [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
CA Query on CA | NA [auth G], R [auth E], SA [auth H], Z [auth F] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | CA [auth C] DA [auth C] EA [auth C] FA [auth C] GA [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
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 Name | Purpose |
---|---|
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
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