5M8S

Crystal structure of human tyrosinase related protein 1 mutant (T391V-R374S-Y362F) in complex with phenylthiourea (PTU)

• PDB DOI: https://doi.org/10.2210/pdb5M8S/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2016-10-29 Released: 2018-01-31 
• Deposition Author(s): Lai, X., Soler-Lopez, M., Wichers, H.J., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.235 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Phenylthiourea Binding to Human Tyrosinase-Related Protein 1

Lai, X., Wichers, H.J., Soler-Lopez, M., Dijkstra, B.W.

(2020) Int J Mol Sci 

• DOI: https://doi.org/10.3390/ijms21030915

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 212.93 kDa 
• Atom Count: 15,622 
• Modelled Residue Count: 1,784 
• Deposited Residue Count: 1,784 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5,6-dihydroxyindole-2-carboxylic acid oxidase	A, B, C, D	446	Homo sapiens	Mutation(s): 3  Gene Names: TYRP1, CAS2, TYRP, TYRRP EC: 1.14.18
UniProt & NIH Common Fund Data Resources
Find proteins for P17643 (Homo sapiens) Explore P17643  Go to UniProtKB:  P17643
PHAROS:  P17643 GTEx:  ENSG00000107165
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: P17643-1

Oligosaccharides

Help

Entity ID: 2
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, H, P	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, J, L, N, O, R, T	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G87612PG GlyCosmos:  G87612PG GlyGen:  G87612PG

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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	K	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G64181RO GlyCosmos:  G64181RO GlyGen:  G64181RO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	M	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-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	Q	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G26032DN GlyCosmos:  G26032DN GlyGen:  G26032DN

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	S	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21381MC GlyCosmos:  G21381MC GlyGen:  G21381MC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	CA [auth C], DA [auth C], EA [auth C], U [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
URS	FA [auth C], IA [auth D], V [auth A], Z [auth B]	N-PHENYLTHIOUREA C7 H8 N2 S FULZLIGZKMKICU-UHFFFAOYSA-N
ZN	AA [auth B], BA [auth B], GA [auth C], HA [auth C], JA [auth D], KA [auth D], W [auth A], X [auth A], Y [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.235 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.081	α = 90
b = 141.767	β = 90
c = 191.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	refinement
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Lai, X., Soler-Lopez, M., Wichers, H.J., Dijkstra, B.W.

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2020-02-12
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary