3D5O

Structural recognition and functional activation of FcrR by innate pentraxins

PDB DOI: https://doi.org/10.2210/pdb3D5O/pdb

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

Deposited: 2008-05-16 Released: 2008-11-11
Deposition Author(s): Lu, J., Marnell, L.L., Marjon, K.D., Mold, C., Du Clos, T.W., Sun, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.279
R-Value Work: 0.207
R-Value Observed: 0.221

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 139.22 kDa
Atom Count: 9,655
Modelled Residue Count: 1,191
Deposited Residue Count: 1,197
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serum amyloid P-component	A, B, C, D, E	204	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02743 (Homo sapiens) Explore P02743 Go to UniProtKB: P02743
PHAROS: P02743 GTEx: ENSG00000132703
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02743
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Low affinity immunoglobulin gamma Fc region receptor II-a	F	177	Homo sapiens	Mutation(s): 0 Gene Names: FCGR2A, CD32, FCG2, FCGR2A1, IGFR2
UniProt & NIH Common Fund Data Resources
Find proteins for P12318 (Homo sapiens) Explore P12318 Go to UniProtKB: P12318
PHAROS: P12318 GTEx: ENSG00000143226
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12318
Sequence Annotations Expand
Reference Sequence

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 J [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E]	J [auth A], N [auth B], R [auth C], V [auth D], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] 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 G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E]	AA [auth F] G [auth A] H [auth A] I [auth A] K [auth B] AA [auth F], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], S [auth D], T [auth D], U [auth D], W [auth E], X [auth E], Y [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth F] MOL2 format, chain BA [auth F]	BA [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Interactions & Density Focus chain BA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.279
R-Value Work: 0.207
R-Value Observed: 0.221
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.197	α = 90
b = 143.477	β = 90
c = 161.588	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-11-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-11-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary