5M8O

Crystal structure of human tyrosinase related protein 1 in complex with tropolone

PDB DOI: https://doi.org/10.2210/pdb5M8O/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: 2.50 Å
R-Value Free: 0.251
R-Value Work: 0.204
R-Value Observed: 0.207

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 214.73 kDa
Atom Count: 15,209
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, U	3		N-Glycosylation	Interactions Focus chain E Focus chain J Focus chain O Focus chain U Interactions & Density Focus chain E Focus chain J Focus chain O Focus chain U
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, Q	2		N-Glycosylation	Interactions Focus chain F Focus chain K Focus chain Q Interactions & Density Focus chain F Focus chain K Focus chain Q
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, R, S, W, Y	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain L Focus chain N Focus chain R Focus chain S Focus chain W Focus chain Y Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain L Focus chain N Focus chain R Focus chain S Focus chain W Focus chain Y
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)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	P, T	3		N-Glycosylation	Interactions Focus chain P Focus chain T Interactions & Density Focus chain P Focus chain T
Glycosylation Resources
GlyTouCan: G19738FR GlyCosmos: G19738FR GlyGen: G19738FR

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0TR Query on 0TR Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain FA [auth C] SDF format, chain IA [auth D] SDF format, chain Z [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain Z [auth A]	CA [auth B], FA [auth C], IA [auth D], Z [auth A]	2-HYDROXYCYCLOHEPTA-2,4,6-TRIEN-1-ONE C₇ H₆ O₂ MDYOLVRUBBJPFM-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain Z [auth A] Interactions & Density Focus chain CA [auth B] Focus chain FA [auth C] Focus chain IA [auth D] Focus chain Z [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain JA [auth D] SDF format, chain KA [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D]	AA [auth A] BA [auth A] DA [auth B] EA [auth B] GA [auth C] AA [auth A], BA [auth A], DA [auth B], EA [auth B], GA [auth C], HA [auth C], JA [auth D], KA [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JA [auth D] Focus chain KA [auth D] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain JA [auth D] Focus chain KA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.251
R-Value Work: 0.204
R-Value Observed: 0.207
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.688	α = 90
b = 140.202	β = 90
c = 191.058	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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