6BE6
ADAM10 Extracellular Domain
- PDB DOI: https://doi.org/10.2210/pdb6BE6/pdb
- Classification: MEMBRANE PROTEIN
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2017-10-24 Released: 2017-12-27 
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.284 
- R-Value Work: 0.236 
- R-Value Observed: 0.239 
wwPDB Validation   3D Report Full Report
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 |
Disintegrin and metalloproteinase domain-containing protein 10 | 449 | Homo sapiens | Mutation(s): 0  Gene Names: ADAM10, KUZ, MADM EC: 3.4.24.81 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O14672 (Homo sapiens) Explore O14672  Go to UniProtKB:  O14672 | |||||
PHAROS:  O14672 GTEx:  ENSG00000137845  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O14672 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G29481IZ GlyCosmos:  G29481IZ GlyGen:  G29481IZ |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G84676UY GlyCosmos:  G84676UY GlyGen:  G84676UY |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | G | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G75436UI GlyCosmos:  G75436UI GlyGen:  G75436UI |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | H | 8 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G00702NP GlyCosmos:  G00702NP GlyGen:  G00702NP |
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
SO4 Query on SO4 | K [auth A] N [auth B] O [auth B] R [auth C] S [auth C] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
ZN Query on ZN | I [auth A], L [auth A], P [auth C], T [auth C] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CA Query on CA | J [auth A], M [auth B], Q [auth C], U [auth D] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.284 
- R-Value Work: 0.236 
- R-Value Observed: 0.239 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 131.42 | α = 90 |
b = 188.78 | β = 90 |
c = 86.64 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data scaling |
PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-12-27  Deposition Author(s): Seegar, T.C.M.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | P41 GM103403 |
Revision History (Full details and data files)
- Version 1.0: 2017-12-27
Type: Initial release - Version 1.1: 2020-01-01
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary