D-I-TASSER P04198

D-I-TASSER results for P04198

[Click result.zip to download all results on this page]

Summary of the Protein

Uniprot ID: P04198
Protein Name: N-myc proto-oncogene protein
Gene Name: MYCN

Input Sequence in FASTA format

>P04198 (464 residues)
MPSCSTSTMPGMICKNPDLEFDSLQPCFYPDEDDFYFGGPDSTPPGEDIWKKFELLPTPP
LSPSRGFAEHSSEPPSWVTEMLLENELWGSPAEEDAFGLGGLGGLTPNPVILQDCMWSGF
SAREKLERAVSEKLQHGRGPPTAGSTAQSPGAGAASPAGRGHGGAAGAGRAGAALPAELA
HPAAECVDPAVVFPFPVNKREPAPVPAAPASAPAAGPAVASGAGIAAPAGAPGVAPPRPG
GRQTSGGDHKALSTSGEDTLSDSDDEDDEEEDEEEEIDVVTVEKRRSSSNTKAVTTFTIT
VRPKNAALGPGRAQSSELILKRCLPIHQQHNYAAPSPYVESEDAPPQKKIKSEASPRPLK
SVIPPKAKSLSPRNSDSEDSERRRNHNILERQRRNDLRSSFLTLRDHVPELVKNEKAAKV
VILKKATEYVHSLQAEEHQLLLEKEKLQARQQQLLKKIEHARTC

Predicted Contact and Distance Map Used in D-I-TASSER simulation

Contact Map

Distance Map

D-I-TASSER simulation is guided by the consensus contact map (left figure) and distance map (right figure) derived based on confidence scores of AttentionPotential. In the contact, distance map and hydrogen bond networks, the axes mark the residue index along the sequence. For the contact map, each dot represents a residue pair with predicted contact, while for the distance map and hydrogen bond network, a color scale represents a distance of 1-20+ angstroms or a angle of 0-180 degree.

Information of Domain

No. of Domain	Domain	Domain Boundary	Length of Domain	Models of Domain	Sequence
1	P04198-D1	1-464	464		MPSCSTSTMPGMICKNPDLEFDSLQPCFYPDEDDFYFGGPDSTPPGEDIWKKFELLPTPPLSPSRGFAEHSSEPPSWVTEMLLENELWGSPAEEDAFGLGGLGGLTPNPVILQDCMWSGFSAREKLERAVSEKLQHGRGPPTAGSTAQSPGAGAASPAGRGHGGAAGAGRAGAALPAELAHPAAECVDPAVVFPFPVNKREPAPVPAAPASAPAAGPAVASGAGIAAPAGAPGVAPPRPGGRQTSGGDHKALSTSGEDTLSDSDDEDDEEEDEEEEIDVVTVEKRRSSSNTKAVTTFTITVRPKNAALGPGRAQSSELILKRCLPIHQQHNYAAPSPYVESEDAPPQKKIKSEASPRPLKSVIPPKAKSLSPRNSDSEDSERRRNHNILERQRRNDLRSSFLTLRDHVPELVKNEKAAKVVILKKATEYVHSLQAEEHQLLLEKEKLQARQQQLLKKIEHARTC

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4314

(a)

D-I-TASSER simulations generate a large ensemble of structural conformations, i.e. decoys. These decoys are clustered by SPICKER based on pairwise structure similarity to report up to five final models from the five largest clusters. Models are ranked in descending order of cluster size. If the simulations converge well, it is possible to have less than 5 models generated, which is usually an indication of good model quality.

(b)

The model confidence is quantitatified by estimated TM-score (eTM-score), calculated based on significance of threading template alignments, contact map satisfaction rate, mean absolute error between distance of model and distance of AttentionPotential, and convergence of D-I-TASSER simulations. eTM-score is typically in the range of [0, 1], with higher eTM-score signifies higher model confidence.

Proteins with similar structure

Top 10 structural analogs in PDB (as identified by TM-align)

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	Download Alignment
1	3zyvA	0.40	7.05	0.048	0.644	model1_3zyvA.pdb.gz
2	2d33A	0.39	6.49	0.080	0.591	model1_2d33A.pdb.gz
3	3ig5A	0.39	7.06	0.055	0.629	model1_3ig5A.pdb.gz
4	3nztA	0.38	6.50	0.052	0.578	model1_3nztA.pdb.gz
5	3ln7A	0.36	6.74	0.055	0.573	model1_3ln7A.pdb.gz
6	4jzaA	0.32	7.60	0.035	0.554	model1_4jzaA.pdb.gz
7	1dgjA2	0.31	7.52	0.043	0.528	model1_1dgjA2.pdb.gz
8	1ffvB3	0.27	6.42	0.014	0.401	model1_1ffvB3.pdb.gz
9	3lmmD	0.23	7.66	0.028	0.394	model1_3lmmD.pdb.gz
10	1xfiA	0.23	6.61	0.050	0.353	model1_1xfiA.pdb.gz

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Gene Ontology (GO) Terms

Molecular Function (MF)

GO term	Cscore^GO	Name
GO:1901363	0.86	heterocyclic compound binding
GO:0097159	0.86	organic cyclic compound binding
GO:0003700	0.85	transcription factor activity, sequence-specific DNA binding
GO:0003676	0.84	nucleic acid binding
GO:0003677	0.83	DNA binding
GO:0000975	0.68	regulatory region DNA binding
GO:0044212	0.67	transcription regulatory region DNA binding
GO:0044877	0.61	macromolecular complex binding
GO:0070888	0.58	E-box binding
GO:0032403	0.57	protein complex binding

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Molecular Function. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Biological Process (BP)

GO term	Cscore^GO	Name
GO:0065007	0.95	biological regulation
GO:0050789	0.95	regulation of biological process
GO:0050794	0.94	regulation of cellular process
GO:0080090	0.91	regulation of primary metabolic process
GO:0060255	0.91	regulation of macromolecule metabolic process
GO:0031323	0.91	regulation of cellular metabolic process
GO:0006355	0.90	regulation of transcription, DNA-templated
GO:0006357	0.86	regulation of transcription from RNA polymerase II promoter
GO:0048522	0.82	positive regulation of cellular process
GO:0044699	0.82	single-organism process
GO:0009987	0.82	cellular process
GO:0009893	0.81	positive regulation of metabolic process
GO:0031325	0.80	positive regulation of cellular metabolic process
GO:0010604	0.80	positive regulation of macromolecule metabolic process
GO:0045893	0.79	positive regulation of transcription, DNA-templated
GO:0048519	0.70	negative regulation of biological process
GO:0045944	0.70	positive regulation of transcription from RNA polymerase II promoter
GO:2000026	0.69	regulation of multicellular organismal development
GO:0048523	0.69	negative regulation of cellular process
GO:0044763	0.69	single-organism cellular process
GO:0008152	0.69	metabolic process
GO:0071704	0.68	organic substance metabolic process
GO:0050896	0.68	response to stimulus
GO:0045595	0.68	regulation of cell differentiation
GO:0044238	0.67	primary metabolic process
GO:0044237	0.66	cellular metabolic process
GO:0043170	0.66	macromolecule metabolic process
GO:0044260	0.65	cellular macromolecule metabolic process
GO:0051241	0.64	negative regulation of multicellular organismal process
GO:0010941	0.64	regulation of cell death
GO:0051716	0.63	cellular response to stimulus
GO:0051093	0.63	negative regulation of developmental process
GO:0045596	0.63	negative regulation of cell differentiation
GO:0042127	0.63	regulation of cell proliferation
GO:0048583	0.62	regulation of response to stimulus
GO:0010942	0.62	positive regulation of cell death
GO:0008284	0.62	positive regulation of cell proliferation
GO:0006950	0.62	response to stress
GO:0065008	0.61	regulation of biological quality
GO:0051246	0.60	regulation of protein metabolic process
GO:0033554	0.60	cellular response to stress
GO:0007165	0.60	signal transduction
GO:0048584	0.59	positive regulation of response to stimulus
GO:0032268	0.59	regulation of cellular protein metabolic process
GO:0016043	0.59	cellular component organization
GO:0009628	0.59	response to abiotic stimulus
GO:0065009	0.58	regulation of molecular function
GO:0051128	0.58	regulation of cellular component organization
GO:0048878	0.58	chemical homeostasis
GO:0044710	0.58	single-organism metabolic process
GO:0043933	0.58	macromolecular complex subunit organization
GO:0042981	0.58	regulation of apoptotic process
GO:0032270	0.58	positive regulation of cellular protein metabolic process
GO:0007166	0.58	cell surface receptor signaling pathway
GO:0080134	0.57	regulation of response to stress
GO:0055072	0.57	iron ion homeostasis
GO:0050790	0.57	regulation of catalytic activity
GO:0033043	0.57	regulation of organelle organization
GO:0030162	0.57	regulation of proteolysis
GO:0009314	0.57	response to radiation
GO:0006996	0.57	organelle organization
GO:0006875	0.57	cellular metal ion homeostasis
GO:0002682	0.57	regulation of immune system process
GO:2001022	0.56	positive regulation of response to DNA damage stimulus
GO:2000573	0.56	positive regulation of DNA biosynthetic process
GO:0060070	0.56	canonical Wnt signaling pathway
GO:0051782	0.56	negative regulation of cell division
GO:0051276	0.56	chromosome organization
GO:0050679	0.56	positive regulation of epithelial cell proliferation
GO:0048146	0.56	positive regulation of fibroblast proliferation
GO:0045656	0.56	negative regulation of monocyte differentiation
GO:0043280	0.56	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0032204	0.56	regulation of telomere maintenance
GO:0010332	0.56	response to gamma radiation
GO:0006974	0.56	cellular response to DNA damage stimulus
GO:0006879	0.56	cellular iron ion homeostasis
GO:0006464	0.56	cellular protein modification process
GO:0006338	0.56	chromatin remodeling
GO:0000165	0.55	MAPK cascade
GO:0009892	0.50	negative regulation of metabolic process

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Biological Process. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Cellular Component (CC)

GO term	Cscore^GO	Name
GO:0044424	1.00	intracellular part
GO:0043229	0.82	intracellular organelle
GO:0043231	0.75	intracellular membrane-bounded organelle
GO:0044422	0.74	organelle part
GO:0044446	0.73	intracellular organelle part
GO:0005634	0.73	nucleus
GO:0044428	0.64	nuclear part
GO:0005654	0.54	nucleoplasm

Download full result of the above consensus prediction.

Click the graph to show a high resolution version.

(a)

Cscore^GO is the confidence score of predicted GO terms. Cscore^GO values range in between [0-1]; where a higher value indicates a better confidence in predicting the function using the template.

(b)

The graph shows the predicted terms within the Gene Ontology hierachy for Cellular Component. Confidently predicted terms are color coded by Cscore^GO:

[0.4,0.5)

[0.5,0.6)

[0.6,0.7)

[0.7,0.8)

[0.8,0.9)

[0.9,1.0]

Predicted Enzyme Commission (EC) Numbers

Top 5 enzyme homologs in PDB

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	EC Number	Predicted Active Site Residues
1	0.060	3ig5A	0.389	7.06	0.055	0.629	6.3.2.2	NA
2	0.060	2ipyA	0.290	7.36	0.023	0.474	4.2.1.3	NA
3	0.060	2fxhA	0.336	7.30	0.066	0.556	1.11.1.7 1.11.1.6	NA
4	0.060	1cjyA	0.333	7.46	0.041	0.567	3.1.1.4 3.1.1.5	NA
5	0.060	1ea0A	0.302	7.37	0.040	0.504	1.4.1.13	NA

	Click on the radio buttons to visualize predicted active site residues.
(a)	Cscore^EC is the confidence score for the Enzyme Commission (EC) number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted Ligand Binding Sites

Template proteins with similar binding site:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.01	1fiqA	0.145	4.88	0.038	0.190	0.58	FES	complex1.pdb.gz	89,90,91,93,98

	Click on the radio buttons to visualize predicted binding site and residues.
(a)	Cscore^LB is the confidence score of predicted binding site. Cscore^LB values range in between [0-1]; where a higher score indicates a more reliable ligand-binding site prediction.
(b)	BS-score is a measure of local similarity (sequence & structure) between template binding site and predicted binding site in the query structure. Based on large scale benchmarking analysis, we have observed that a BS-score >1 reflects a significant local match between the predicted and template binding site.
(c)	TM-score is a measure of global structural similarity between query and template protein.
(d)	RMSD^a the RMSD between residues that are structurally aligned by TM-align.
(e)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(f)	Cov. represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

[Click result.zip to download all results on this page]

References:
1.	Wei Zheng, Chengxin Zhang, Yang Li, Robin Pearce, Eric W. Bell, Yang Zhang. Folding non-homology proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. In preparation, 2020.