D-I-TASSER A2A3K4

D-I-TASSER results for A2A3K4

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

Summary of the Protein

Uniprot ID: A2A3K4
Protein Name: Protein tyrosine phosphatase domain-containing protein 1
Gene Name: PTPDC1

Input Sequence in FASTA format

>A2A3K4 (754 residues)
MAAGVLPQNEQPYSTLVNNSECVANMKGNLERPTPKYTKVGERLRHVIPGHMACSMACGG
RACKYENPARWSEQEQAIKGVYSSWVTDNILAMARPSSELLEKYHIIDQFLSHGIKTIIN
LQRPGEHASCGNPLEQESGFTYLPEAFMEAGIYFYNFGWKDYGVASLTTILDMVKVMTFA
LQEGKVAIHCHAGLGRTGVLIACYLVFATRMTADQAIIFVRAKRPNSIQTRGQLLCVREF
TQFLTPLRNIFSCCDPKAHAVTLPQYLIRQRHLLHGYEARLLKHVPKIIHLVCKLLLDLA
ENRPVMMKDVSEGPGLSAEIEKTMSEMVTMQLDKELLRHDSDVSNPPNPTAVAADFDNRG
MIFSNEQQFDPLWKRRNVECLQPLTHLKRRLSYSDSDLKRAENLLEQGETPQTVPAQILV
GHKPRQQKLISHCYIPQSPEPDLHKEALVRSTLSFWSQSKFGGLEGLKDNGSPIFHGRII
PKEAQQSGAFSADVSGSHSPGEPVSPSFANVHKDPNPAHQQVSHCQCKTHGVGSPGSVRQ
NSRTPRSPLDCGSSPKAQFLVEHETQDSKDLSEAASHSALQSELSAEARRILAAKALANL
NESVEKEELKRKVEMWQKELNSRDGAWERICGERDPFILCSLMWSWVEQLKEPVITKEDV
DMLVDRRADAAEALFLLEKGQHQTILCVLHCIVNLQTIPVDVEEAFLAHAIKAFTKVNFD
SENGPTVYNTLKKIFKHTLEEKRKMTKDGPKPGL

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 DeepPotential. 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	A2A3K4-D1	1-248	248		MAAGVLPQNEQPYSTLVNNSECVANMKGNLERPTPKYTKVGERLRHVIPGHMACSMACGGRACKYENPARWSEQEQAIKGVYSSWVTDNILAMARPSSELLEKYHIIDQFLSHGIKTIINLQRPGEHASCGNPLEQESGFTYLPEAFMEAGIYFYNFGWKDYGVASLTTILDMVKVMTFALQEGKVAIHCHAGLGRTGVLIACYLVFATRMTADQAIIFVRAKRPNSIQTRGQLLCVREFTQFLTPLR
2	A2A3K4-D2	249-317	69		NIFSCCDPKAHAVTLPQYLIRQRHLLHGYEARLLKHVPKIIHLVCKLLLDLAENRPVMMKDVSEGPGLS
3	A2A3K4-D3	318-385	68		AEIEKTMSEMVTMQLDKELLRHDSDVSNPPNPTAVAADFDNRGMIFSNEQQFDPLWKRRNVECLQPLT
4	A2A3K4-D4	386-478	93		HLKRRLSYSDSDLKRAENLLEQGETPQTVPAQILVGHKPRQQKLISHCYIPQSPEPDLHKEALVRSTLSFWSQSKFGGLEGLKDNGSPIFHGR
5	A2A3K4-D5	479-580	102		IIPKEAQQSGAFSADVSGSHSPGEPVSPSFANVHKDPNPAHQQVSHCQCKTHGVGSPGSVRQNSRTPRSPLDCGSSPKAQFLVEHETQDSKDLSEAASHSAL
6	A2A3K4-D6	581-651	71		QSELSAEARRILAAKALANLNESVEKEELKRKVEMWQKELNSRDGAWERICGERDPFILCSLMWSWVEQLK
7	A2A3K4-D7	652-754	103		EPVITKEDVDMLVDRRADAAEALFLLEKGQHQTILCVLHCIVNLQTIPVDVEEAFLAHAIKAFTKVNFDSENGPTVYNTLKKIFKHTLEEKRKMTKDGPKPGL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.727

(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 DeepPotential, 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	2vdcA	0.33	8.38	0.050	0.528	model1_2vdcA.pdb.gz
2	5yz0A	0.33	8.41	0.038	0.530	model1_5yz0A.pdb.gz
3	7bdiB	0.33	8.32	0.056	0.515	model1_7bdiB.pdb.gz
4	5m59A	0.33	8.12	0.046	0.507	model1_5m59A.pdb.gz
5	6uebA	0.32	8.55	0.047	0.515	model1_6uebA.pdb.gz
6	7biiA	0.32	8.24	0.040	0.500	model1_7biiA.pdb.gz
7	6z2wE	0.32	7.65	0.037	0.483	model1_6z2wE.pdb.gz
8	5gm6B	0.32	8.15	0.064	0.493	model1_5gm6B.pdb.gz
9	5n0bA	0.31	8.64	0.033	0.520	model1_5n0bA.pdb.gz
10	7nj0A	0.31	8.14	0.046	0.484	model1_7nj0A.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:0016791	1.00	phosphatase activity
GO:0004721	0.94	phosphoprotein phosphatase activity
GO:0004725	0.93	protein tyrosine phosphatase activity
GO:0097159	0.58	organic cyclic compound binding
GO:1901363	0.57	heterocyclic compound 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:0009987	0.96	cellular process
GO:0044699	0.88	single-organism process
GO:0044763	0.87	single-organism cellular process
GO:0016043	0.84	cellular component organization
GO:0044767	0.82	single-organism developmental process
GO:0030030	0.81	cell projection organization
GO:0048869	0.71	cellular developmental process
GO:0009653	0.69	anatomical structure morphogenesis
GO:0060271	0.68	cilium morphogenesis
GO:0065007	0.60	biological regulation
GO:0050789	0.59	regulation of biological process
GO:0050794	0.58	regulation of cellular 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	0.99	intracellular organelle
GO:0043231	0.98	intracellular membrane-bounded organelle
GO:0005737	0.96	cytoplasm
GO:0005634	0.96	nucleus

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	1ea0A	0.328	8.64	0.043	0.536	1.4.1.13	702
2	0.060	1llwA	0.292	8.45	0.043	0.472	1.4.7.1	NA
3	0.060	1f1sA	0.264	8.60	0.052	0.435	4.2.2.1	NA
4	0.060	2vdcA	0.330	8.38	0.050	0.528	1.4.1.13	NA
5	0.060	3b9jC	0.245	8.76	0.036	0.403	1.17.3.2 1.17.1.4	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:

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	1n1hA	0.303	8.22	0.032	0.479	0.17	UUU	complex1.pdb.gz	114,115,117,118
2	0.01	1n1hA	0.303	8.22	0.032	0.479	0.11	QNA	complex2.pdb.gz	79,81,82,130
3	0.01	1ofdA	0.275	8.07	0.037	0.428	0.19	FMN	complex3.pdb.gz	78,80,109,193
4	0.01	1llzA	0.276	8.13	0.048	0.431	0.15	FMN	complex4.pdb.gz	193,227,228
5	0.01	1xmvA	0.137	5.91	0.038	0.180	0.16	ADP	complex5.pdb.gz	70,71,192,194
6	0.01	1ofdA	0.275	8.07	0.037	0.428	0.30	F3S	complex6.pdb.gz	97,102,104,106,107
7	0.01	3cmvG	0.259	8.26	0.047	0.411	0.19	ANP	complex7.pdb.gz	109,110,111,112
8	0.01	3cmvA	0.263	8.39	0.050	0.424	0.10	ANP	complex8.pdb.gz	86,115,119
9	0.01	2nm1A	0.181	7.79	0.033	0.279	0.17	III	complex9.pdb.gz	85,86,184,185,186,187,193
10	0.01	3cmvB	0.257	8.23	0.047	0.410	0.16	ANP	complex10.pdb.gz	83,84,85,110,113

	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, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Yiheng Zhu, P. Lydia Freddolino, Yang Zhang. Integrating deep learning potentials with I-TASSER for single- and multi-domain protein structure prediction. Submitted. 2023.