6VFR
Crystal structure of human protocadherin 18 EC1-EC4
- PDB DOI: https://doi.org/10.2210/pdb6VFR/pdb
- Classification: CELL ADHESION
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2020-01-06 Released: 2020-03-11 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.79 Å
- R-Value Free: 0.272 
- R-Value Work: 0.236 
- R-Value Observed: 0.238 
wwPDB Validation   3D Report Full Report
Currently 6VFR does not have a validation slider image.
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Protocadherin-18 | 436 | Homo sapiens | Mutation(s): 0  Gene Names: PCDH18, KIAA1562 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9HCL0 (Homo sapiens) Explore Q9HCL0  Go to UniProtKB:  Q9HCL0 | |||||
PHAROS:  Q9HCL0 GTEx:  ENSG00000189184  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9HCL0 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | C | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G80587NA GlyCosmos:  G80587NA GlyGen:  G80587NA |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | E | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB |
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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | F | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | V [auth B], W [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
EDO Query on EDO | GA [auth B] HA [auth B] IA [auth B] P [auth A] Q [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
CA Query on CA | AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
NA Query on NA | JA [auth B], U [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.79 Å
- R-Value Free: 0.272 
- R-Value Work: 0.236 
- R-Value Observed: 0.238 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 126.959 | α = 90 |
b = 176.942 | β = 101.423 |
c = 71.872 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Structure Validation
View Full Validation Report
Currently 6VFR does not have a validation slider image.
Entry History & Funding Information
Deposition Data
- Released Date: 2020-03-11  Deposition Author(s): Harrison, O.J., Brasch, J., Shapiro, L.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01MH114817 |
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | R01GM118584 |
National Science Foundation (NSF, United States) | United States | MCB-1412472 |
Revision History (Full details and data files)
- Version 1.0: 2020-03-11
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary