5M8L

Crystal structure of human tyrosinase related protein 1

PDB DOI: https://doi.org/10.2210/pdb5M8L/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2016-10-29 Released: 2017-07-12
Deposition Author(s): Lai, X., Soler-Lopez, M., Wichers, H.J., Dijkstra, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.255
R-Value Work: 0.214
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 213.57 kDa
Atom Count: 15,126
Modelled Residue Count: 1,784
Deposited Residue Count: 1,784
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17643
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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, J, O, S	3		N-Glycosylation	Interactions Focus chain E Focus chain J Focus chain O Focus chain S Interactions & Density Focus chain E Focus chain J Focus chain O Focus chain S
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, K, P	2		N-Glycosylation	Interactions Focus chain F Focus chain K Focus chain P Interactions & Density Focus chain F Focus chain K Focus chain P
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, L, N G, H, I, L, N, Q, R, U, W	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain L Focus chain N Focus chain Q Focus chain R Focus chain U Focus chain W Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain L Focus chain N Focus chain Q Focus chain R Focus chain U Focus chain W
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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	M	6		N-Glycosylation	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G64181RO GlyCosmos: G64181RO GlyGen: G64181RO

Entity ID: 6
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	T	5		N-Glycosylation	Interactions Focus chain T Interactions & Density Focus chain T
Glycosylation Resources
GlyTouCan: G26032DN GlyCosmos: G26032DN GlyGen: G26032DN

Entity ID: 7
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	V	5		N-Glycosylation	Interactions Focus chain V Interactions & Density Focus chain V
Glycosylation Resources
GlyTouCan: G21381MC GlyCosmos: G21381MC GlyGen: G21381MC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C]	CA [auth C], DA [auth C]	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] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain Z [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A]	AA [auth B] BA [auth B] EA [auth C] FA [auth C] GA [auth D] AA [auth B], BA [auth B], EA [auth C], FA [auth C], GA [auth D], HA [auth D], X [auth A], Y [auth A], Z [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.255
R-Value Work: 0.214
R-Value Observed: 0.216
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.424	α = 90
b = 141.758	β = 90
c = 191.741	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-07-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-12
Type: Initial release
Version 1.1: 2017-08-09
Changes: Database references
Version 1.2: 2019-10-16
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary