9G6W | pdb_00009g6w

L-SIGN CRD in complex with Man96.

PDB DOI: https://doi.org/10.2210/pdb9G6W/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-19 Released: 2025-07-30
Deposition Author(s): Thepaut, M., Cavazzoli, G., Bernardi, A., Fieschi, F.
Funding Organization(s): Grenoble Alliance for Integrated Structural Cell Biology (GRAL), Ministero dell Universita e della Ricerca

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.290 (Depositor), 0.320 (DCC)
R-Value Work:
0.228 (Depositor), 0.264 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

L-SIGN CRD in complex with Man96.

Cavazzoli, G., Pollastri, S., Panzeri, A., Sattin, S., Belvisi, L., Bernardi, A., Delaunay, C., Thepaut, M., Fieschi, F.

To be published.

Macromolecule Content

Total Structure Weight: 32.83 kDa
Atom Count: 2,304
Modeled Residue Count: 256
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 1 of C-type lectin domain family 4 member M	A, B	137	Homo sapiens	Mutation(s): 0 Gene Names: CLEC4M, CD209L, CD209L1, CD299
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2X3 (Homo sapiens) Explore Q9H2X3 Go to UniProtKB: Q9H2X3
PHAROS: Q9H2X3 GTEx: ENSG00000104938
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H2X3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IIW (Subject of Investigation/LOI) Query on A1IIW Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(2-chloroethyloxy)-2-(hydroxymethyl)-5-[4-[(imidazolidin-2-ylideneamino)methyl]-1,2,3-triazol-1-yl]oxane-3,4-diol C₁₄ H₂₃ Cl N₆ O₅ SUTPIBBHKSRFDY-MLGHIDQZSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	D [auth A] E [auth A] F [auth A] J [auth B] K [auth B] D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.290 (Depositor), 0.320 (DCC)
R-Value Work: 0.228 (Depositor), 0.264 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.72	α = 90
b = 105.72	β = 90
c = 59.11	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)	France	CBH-EUR-GS (ANR-17- EURE0003)
Ministero dell Universita e della Ricerca	Italy	PRIN 20224LLK82