4R9J

L-ficolin complexed to glucosamine-6-sulfate

PDB DOI: https://doi.org/10.2210/pdb4R9J/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: unidentified baculovirus
Mutation(s): No

Deposited: 2014-09-05 Released: 2014-11-05
Deposition Author(s): Laffly, E., Lacroix, M., Martin, L., Vassal-Stermann, E., Thielens, N., Gaboriaud, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.203
R-Value Work: 0.172
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Human ficolin-2 recognition versatility extended: An update on the binding of ficolin-2 to sulfated/phosphated carbohydrates.

Laffly, E., Lacroix, M., Martin, L., Vassal-Stermann, E., Thielens, N.M., Gaboriaud, C.

(2014) FEBS Lett 588: 4694-4700

PubMed: 25447524 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2014.10.042
Primary Citation of Related Structures:
4R9J, 4R9T

PubMed Abstract:
Ficolin-2 has been reported to bind to DNA and heparin, but the mechanism involved has not been thoroughly investigated. X-ray studies of the ficolin-2 fibrinogen-like domain in complex with several new ligands now show that sulfate and phosphate groups are prone to bind to the S3 binding site of the protein. Composed of Arg132, Asp133, Thr136 and Lys221, the S3 site was previously shown to mainly bind N-acetyl groups. Furthermore, DNA and heparin compete for binding to ficolin-2. Mutagenesis studies reveal that Arg132, and to a lesser extent Asp133, are important for this binding property. The versatility of the S3 site in binding N-acetyl, sulfate and phosphate groups is discussed through comparisons with homologous fibrinogen-like recognition proteins.

Organizational Affiliation

Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France.

Macromolecule Content

Total Structure Weight: 76.09 kDa
Atom Count: 5,653
Modelled Residue Count: 651
Deposited Residue Count: 651
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ficolin-2	A [auth G], B [auth A], C [auth B]	217	Homo sapiens	Mutation(s): 0 Gene Names: FCN2, FCNL
UniProt & NIH Common Fund Data Resources
Find proteins for Q15485 (Homo sapiens) Explore Q15485 Go to UniProtKB: Q15485
PHAROS: Q15485 GTEx: ENSG00000160339
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15485
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth G] Focus chain B [auth A]	Go to GlyGen: Q15485-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	3		N-Glycosylation	Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3LJ Query on 3LJ Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain N [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	N [auth A], S [auth B], T [auth B]	2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose C₆ H₁₃ N O₈ S MTDHILKWIRSIHB-UKFBFLRUSA-N		Interactions Focus chain N [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain N [auth A] Focus chain S [auth B] Focus chain T [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth G] MOL2 format, chain I [auth G] mmCIF format, chain I [auth G]	I [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth G] Interactions & Density Focus chain I [auth G]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth G] SDF format, chain G SDF format, chain H [auth G] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain P [auth B] MOL2 format, chain F [auth G] MOL2 format, chain G MOL2 format, chain H [auth G] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] mmCIF format, chain F [auth G] mmCIF format, chain G mmCIF format, chain H [auth G] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B]	F [auth G] G H [auth G] K [auth A] L [auth A] F [auth G], G, H [auth G], K [auth A], L [auth A], P [auth B], R [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain R [auth B] Interactions & Density Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain R [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth G] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] MOL2 format, chain E [auth G] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain E [auth G] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B]	E [auth G], J [auth A], M [auth A], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth G] Focus chain J [auth A] Focus chain M [auth A] Focus chain Q [auth B] Interactions & Density Focus chain E [auth G] Focus chain J [auth A] Focus chain M [auth A] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.203
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.17	α = 90
b = 97.17	β = 90
c = 139.99	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-11-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-05
Type: Initial release
Version 1.1: 2014-12-17
Changes: Database references
Version 1.2: 2015-01-14
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-10-30
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4R9J

L-ficolin complexed to glucosamine-6-sulfate

Human ficolin-2 recognition versatility extended: An update on the binding of ficolin-2 to sulfated/phosphated carbohydrates.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)