OCA Atlas for 5M8Q

5M8Q

Unknown Function

date

Oct 29, 2016

title

Crystal Structure Of Human Tyrosinase Related Protein 1 Muta R374s-Y362f) In Complex With Kojic Acid

authors

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

compound

source

Molecule: 5,6-Dihydroxyindole-2-Carboxylic Acid Oxidase
Chain: A, B, C, D
Synonym: Dhica Oxidase,Catalase B,Glycoprotein 75,Melanoma Gp75,Tyrosinase-Related Protein 1,Trp1;
Ec: 1.14.18.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tyrp1, Cas2, Tyrp, Tyrrp
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

symmetry

Space Group: P 21 21 21

R_factor

0.208

R_Free

0.275

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
89.640	140.426	191.559	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.85 Å

ligand

FUC, KOJ, MAN, NAG, ZN

enzyme

Oxidoreductase E.C.1.14.18 BRENDA

Gene
Ontology

Chain	Function	Process	Component
A, D, C, B

Primary reference

Structure of Human Tyrosinase Related Protein 1 Reveals a Binuclear Zinc Active Site Important for Melanogenesis., Lai X, Wichers HJ, Soler-Lopez M, Dijkstra BW, Angew Chem Int Ed Engl. 2017 Aug 7;56(33):9812-9815. doi: 10.1002/anie.201704616., Epub 2017 Jul 17. PMID:28661582

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (300 Kb) [Save to disk]

Biological Unit Coordinates (5m8q.pdb1.gz) 77 Kb

Biological Unit Coordinates (5m8q.pdb2.gz) 75 Kb

Biological Unit Coordinates (5m8q.pdb3.gz) 77 Kb

Biological Unit Coordinates (5m8q.pdb4.gz) 76 Kb

LPC: Ligand-Protein Contacts for 5M8Q

CSU: Contacts of Structural Units for 5M8Q

Structure Factors (1171 Kb)

Retrieve 5M8Q in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5M8Q from S2C, [Save to disk]

Re-refined 5m8q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5M8Q in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 5M8Q

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5m8q_A] [5m8q_D] [5m8q_B] [5m8q_C]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 5M8Q

Community annotation for 5M8Q at PDBWiki (http://pdbwiki.org)

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]