D-I-TASSER P04637

D-I-TASSER results for P04637

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

Summary of the Protein

Uniprot ID: P04637
Protein Name: Cellular tumor antigen p53
Gene Name: TP53

Input Sequence in FASTA format

>P04637 (393 residues)
MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP
PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

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	P04637-D1	1-393	393		MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.6121

(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	6lhdA	0.62	2.57	0.690	0.662	model1_6lhdA.pdb.gz
2	2rmnA	0.50	2.27	0.476	0.527	model1_2rmnA.pdb.gz
3	2bimA	0.49	0.66	0.974	0.496	model1_2bimA.pdb.gz
4	5dmyA	0.42	6.68	0.044	0.654	model1_5dmyA.pdb.gz
5	5h3zA	0.42	6.63	0.058	0.684	model1_5h3zA.pdb.gz
6	6ysqA	0.41	6.45	0.067	0.636	model1_6ysqA.pdb.gz
7	7abis	0.41	6.54	0.044	0.667	model1_7abis.pdb.gz
8	6xreM	0.41	5.04	0.582	0.547	model1_6xreM.pdb.gz
9	4bgdA	0.41	6.83	0.047	0.674	model1_4bgdA.pdb.gz
10	5m59A	0.41	6.69	0.061	0.669	model1_5m59A.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:0003676	0.97	nucleic acid binding
GO:0003677	0.96	DNA binding
GO:0003700	0.84	transcription factor activity, sequence-specific DNA binding
GO:0043565	0.81	sequence-specific DNA binding
GO:0003690	0.81	double-stranded DNA binding
GO:0044877	0.57	macromolecular complex binding
GO:0003682	0.56	chromatin binding
GO:0003684	0.55	damaged DNA binding
GO:0002039	0.54	p53 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:0050794	1.00	regulation of cellular process
GO:0048523	0.96	negative regulation of cellular process
GO:0050896	0.94	response to stimulus
GO:0009987	0.94	cellular process
GO:0006355	0.91	regulation of transcription, DNA-templated
GO:0033554	0.89	cellular response to stress
GO:0048518	0.88	positive regulation of biological process
GO:0048522	0.87	positive regulation of cellular process
GO:2000113	0.86	negative regulation of cellular macromolecule biosynthetic process
GO:0045934	0.86	negative regulation of nucleobase-containing compound metabolic process
GO:0010629	0.86	negative regulation of gene expression
GO:0045892	0.85	negative regulation of transcription, DNA-templated
GO:0042981	0.82	regulation of apoptotic process
GO:0031325	0.81	positive regulation of cellular metabolic process
GO:0006974	0.81	cellular response to DNA damage stimulus
GO:0045893	0.80	positive regulation of transcription, DNA-templated
GO:0006357	0.80	regulation of transcription from RNA polymerase II promoter
GO:0045944	0.79	positive regulation of transcription from RNA polymerase II promoter
GO:0009314	0.79	response to radiation
GO:0009416	0.78	response to light stimulus
GO:0044699	0.71	single-organism process
GO:0007165	0.65	signal transduction
GO:0097193	0.63	intrinsic apoptotic signaling pathway
GO:0032502	0.62	developmental process
GO:0044767	0.61	single-organism developmental process
GO:0048583	0.59	regulation of response to stimulus
GO:0023051	0.58	regulation of signaling
GO:0010646	0.58	regulation of cell communication
GO:0008152	0.58	metabolic process
GO:0071704	0.56	organic substance metabolic process
GO:0043065	0.56	positive regulation of apoptotic process
GO:0051726	0.55	regulation of cell cycle
GO:0044763	0.55	single-organism cellular process
GO:0044238	0.55	primary metabolic process
GO:0044237	0.55	cellular metabolic process
GO:0022402	0.55	cell cycle process
GO:0009966	0.55	regulation of signal transduction
GO:1903047	0.54	mitotic cell cycle process
GO:0071478	0.54	cellular response to radiation
GO:0045786	0.54	negative regulation of cell cycle
GO:0043170	0.54	macromolecule metabolic process
GO:0042771	0.54	intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
GO:0030330	0.54	DNA damage response, signal transduction by p53 class mediator
GO:0010564	0.54	regulation of cell cycle process
GO:0010332	0.54	response to gamma radiation
GO:0009411	0.54	response to UV
GO:0007346	0.54	regulation of mitotic cell cycle
GO:0044260	0.53	cellular macromolecule metabolic process
GO:0043523	0.53	regulation of neuron apoptotic process
GO:0034644	0.53	cellular response to UV
GO:0033043	0.53	regulation of organelle organization
GO:0031571	0.53	mitotic G1 DNA damage checkpoint
GO:0010165	0.53	response to X-ray
GO:0006978	0.53	DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
GO:0000122	0.53	negative regulation of transcription from RNA polymerase II promoter
GO:0010638	0.52	positive regulation of organelle organization
GO:0034641	0.51	cellular nitrogen compound metabolic process
GO:0090304	0.50	nucleic acid 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:0044446	0.83	intracellular organelle part
GO:0044444	0.83	cytoplasmic part
GO:0043226	0.81	organelle
GO:0043229	0.80	intracellular organelle
GO:0043227	0.80	membrane-bounded organelle
GO:0043231	0.79	intracellular membrane-bounded organelle
GO:0005634	0.70	nucleus
GO:0032991	0.62	macromolecular complex
GO:0043234	0.59	protein complex
GO:0005829	0.57	cytosol
GO:0005667	0.55	transcription factor complex
GO:0044427	0.53	chromosomal part
GO:0000785	0.52	chromatin
GO:0044428	0.50	nuclear part

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	3fn9C	0.385	6.66	0.059	0.613	3.2.1.23	NA
2	0.060	1bglA	0.403	6.44	0.065	0.634	3.2.1.23	NA
3	0.060	1zpuA	0.357	6.87	0.027	0.598	1.-.-.-	NA
4	0.060	3eifA	0.384	6.47	0.048	0.590	3.4.21.110	NA
5	0.060	1ug9A	0.389	6.63	0.035	0.626	3.2.1.70	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	0.43	2ahiC	0.488	0.58	1.000	0.491	1.55	QNA	complex1.pdb.gz	120,239,241,273,275,276,277,280

	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.