5M8S | pdb_00005m8s

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.235 (Depositor), 0.237 (DCC)
R-Value Work:
0.194 (Depositor), 0.199 (DCC)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17643
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P17643-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain E Focus chain H Focus chain P Interactions & Density Focus chain E Focus chain H Focus chain P
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G64181RO GlyCosmos: G64181RO GlyGen: G64181RO

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

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain Q Interactions & Density Focus chain Q
Glycosylation Resources
GlyTouCan: G26032DN GlyCosmos: G26032DN GlyGen: G26032DN

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain S Interactions & Density Focus chain S
Glycosylation Resources
GlyTouCan: G21381MC GlyCosmos: G21381MC GlyGen: G21381MC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain U [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain U [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain U [auth A]	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		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain U [auth A] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain U [auth A]
URS Query on URS Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain V [auth A] SDF format, chain IA [auth D] SDF format, chain FA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain V [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain FA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain V [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain FA [auth C]	FA [auth C], IA [auth D], V [auth A], Z [auth B]	N-PHENYLTHIOUREA C₇ H₈ N₂ S FULZLIGZKMKICU-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain IA [auth D] Focus chain V [auth A] Focus chain Z [auth B] Interactions & Density Focus chain FA [auth C] Focus chain IA [auth D] Focus chain V [auth A] Focus chain Z [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain KA [auth D] SDF format, chain JA [auth D] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] GA [auth C] HA [auth C] JA [auth D] 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		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.235 (Depositor), 0.237 (DCC)
R-Value Work: 0.194 (Depositor), 0.199 (DCC)
R-Value Observed: 0.196 (Depositor)

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

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-01-31

Deposition Author(s):

Revision History (Full details and data files)

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