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6ghv

Structure of a DC-SIGN CRD in complex with high affinity glycomimetic.

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CD209 antigen

Homo sapiens

UniProt Q9NNX6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 ;[1-[(2~{S},3~{S},4~{R},5~{S},6~{R})-2-[(1~{S},2~{S},4~{S},5~{S})-2-(2-chloroethyloxy)-4,5-bis[[4-(hydroxymethyl)phenyl]methylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methylazanium ; × 1 CALCIUM ION × 3 CHLORIDE ION × 3 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 ;[1-[(2~{S},3~{S},4~{R},5~{S},6~{R})-2-[(1~{S},2~{S},4~{S},5~{S})-2-(2-chloroethyloxy)-4,5-bis[[4-(hydroxymethyl)phenyl]methylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methylazanium ; × 1 CALCIUM ION × 3 CHLORIDE ION × 2 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 ;[1-[(2~{S},3~{S},4~{R},5~{S},6~{R})-2-[(1~{S},2~{S},4~{S},5~{S})-2-(2-chloroethyloxy)-4,5-bis[[4-(hydroxymethyl)phenyl]methylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methylazanium ; × 1 CALCIUM ION × 3 CHLORIDE ION × 2 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 ;[1-[(2~{S},3~{S},4~{R},5~{S},6~{R})-2-[(1~{S},2~{S},4~{S},5~{S})-2-(2-chloroethyloxy)-4,5-bis[[4-(hydroxymethyl)phenyl]methylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methylazanium ; × 1 CALCIUM ION × 3 CHLORIDE ION × 2 water × 1 Consistent with protein count
5 Protein monomer Monomer Protein 1 ;[1-[(2~{S},3~{S},4~{R},5~{S},6~{R})-2-[(1~{S},2~{S},4~{S},5~{S})-2-(2-chloroethyloxy)-4,5-bis[[4-(hydroxymethyl)phenyl]methylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methylazanium ; × 1 CALCIUM ION × 3 CHLORIDE ION × 3 water × 1 Consistent with protein count
6 Protein monomer Monomer Protein 1 ;[1-[(2~{S},3~{S},4~{R},5~{S},6~{R})-2-[(1~{S},2~{S},4~{S},5~{S})-2-(2-chloroethyloxy)-4,5-bis[[4-(hydroxymethyl)phenyl]methylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methylazanium ; × 1 CALCIUM ION × 3 CHLORIDE ION × 2 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2xr5 2xr6 6ghv 6ghv 6ghv 6ghv 6ghv 6ghv 7nl6 7nl7 9emq 9emr

15 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2it5 2it6

2 assemblies

View Construct and Data Evidence
UniProt name CD209_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–155； UniProt 250–404 Author chain B； PDBConstruct 1–155； UniProt 250–404 Author chain C； PDBConstruct 1–155； UniProt 250–404 Author chain D； PDBConstruct 1–155； UniProt 250–404 Author chain E； PDBConstruct 1–155； UniProt 250–404 Author chain F； PDBConstruct 1–155； UniProt 250–404

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ghv
Deposition date deposition_date2018-05-09
Structure title titleStructure of a DC-SIGN CRD in complex with high affinity glycomimetic.
Keywords keywordsDC-SIGN, Inhibitor, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6ghv__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6ghv__assembly_3__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6ghv__assembly_3__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）15.74 Å
Rg (electron density)14.73 Å
Total Rg15.96 Å
Atom count1135
Residues133
Excluded volume19914 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6ghv__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6ghv__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6ghv__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 6ghv__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 6ghv__assembly_5__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 6ghv__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6ghva_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd6ghvb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd6ghvc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd6ghvd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd6ghve_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd6ghvf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain

CATH v4.4 (6 domains)

Domain ID domain_id6ghvA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id6ghvB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id6ghvC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id6ghvD00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id6ghvE00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id6ghvF00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
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7. Citations (1)