D-I-TASSER Q8NDZ4

D-I-TASSER results for Q8NDZ4

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

Summary of the Protein

Uniprot ID: Q8NDZ4
Protein Name: Divergent protein kinase domain 2A
Gene Name: DIPK2A

Input Sequence in FASTA format

>Q8NDZ4 (430 residues)
MWRLVPPKLGRLSRSLKLAALGSLLVLMVLHSPSLLASWQRNELTDRRFLQLNKCPACFG
TSWCRRFLNGQVVFEAWGRLRLLDFLNVKNVYFAQYGEPREGGRRRVVLKRLGSQRELAQ
LDQSICKRATGRPRCDLLQAMPRTEFARLNGDVRLLTPEAVEGWSDLVHCPSQRLLDRLV
RRYAETKDSGSFLLRNLKDSERMQLLLTLAFNPEPLVLQSFPSDEGWPFAKYLGACGRMV
AVNYVGEELWSYFNAPWEKRVDLAWQLMEIAEQLTNNDFEFALYLLDVSFDNFAVGPRDG
KVIIVDAENVLVADKRLIRQNKPENWDVWYESKFDDCDKEACLSFSKEILCARATVDHNY
YAVCQNLLSRHATWRGTSGGLLHDPPSEIAKDGRLEALLDECANPKKRYGRFQAAKELRE
YLAQLSNNVR

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	Q8NDZ4-D1	1-245	245		MWRLVPPKLGRLSRSLKLAALGSLLVLMVLHSPSLLASWQRNELTDRRFLQLNKCPACFGTSWCRRFLNGQVVFEAWGRLRLLDFLNVKNVYFAQYGEPREGGRRRVVLKRLGSQRELAQLDQSICKRATGRPRCDLLQAMPRTEFARLNGDVRLLTPEAVEGWSDLVHCPSQRLLDRLVRRYAETKDSGSFLLRNLKDSERMQLLLTLAFNPEPLVLQSFPSDEGWPFAKYLGACGRMVAVNYV
2	Q8NDZ4-D2	246-430	185		GEELWSYFNAPWEKRVDLAWQLMEIAEQLTNNDFEFALYLLDVSFDNFAVGPRDGKVIIVDAENVLVADKRLIRQNKPENWDVWYESKFDDCDKEACLSFSKEILCARATVDHNYYAVCQNLLSRHATWRGTSGGLLHDPPSEIAKDGRLEALLDECANPKKRYGRFQAAKELREYLAQLSNNVR

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.75

(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	6j5tH	0.50	4.35	0.090	0.616	model1_6j5tH.pdb.gz
2	7nurA	0.49	5.49	0.070	0.674	model1_7nurA.pdb.gz
3	3q5zA	0.48	4.39	0.113	0.598	model1_3q5zA.pdb.gz
4	3dlsA	0.48	4.19	0.084	0.588	model1_3dlsA.pdb.gz
5	4l68A	0.47	4.68	0.084	0.602	model1_4l68A.pdb.gz
6	7kpvA	0.47	4.55	0.096	0.588	model1_7kpvA.pdb.gz
7	4myiA	0.47	4.80	0.079	0.605	model1_4myiA.pdb.gz
8	7akgA	0.47	4.33	0.103	0.574	model1_7akgA.pdb.gz
9	4f99A	0.47	4.31	0.097	0.577	model1_4f99A.pdb.gz
10	4oa2A	0.47	4.17	0.079	0.570	model1_4oa2A.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:0003824	0.78	catalytic activity
GO:0016740	0.72	transferase activity
GO:0016773	0.70	phosphotransferase activity, alcohol group as acceptor
GO:0016301	0.70	kinase activity
GO:1901363	0.59	heterocyclic compound binding
GO:0097159	0.59	organic cyclic compound binding
GO:0035639	0.56	purine ribonucleoside triphosphate binding
GO:0032555	0.56	purine ribonucleotide binding
GO:0032550	0.56	purine ribonucleoside binding
GO:0032559	0.54	adenyl ribonucleotide 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:0009966	1.00	regulation of signal transduction
GO:0044699	0.73	single-organism process
GO:0060038	0.66	cardiac muscle cell proliferation
GO:0014066	0.66	regulation of phosphatidylinositol 3-kinase signaling

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:0030126	1.00	COPI vesicle coat
GO:0005615	1.00	extracellular space

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	0.066	1xqzA	0.454	4.15	0.089	0.556	2.7.11.1 2.7.1.37	NA
2	0.066	3dlsA	0.478	4.19	0.084	0.588	2.7.11.1	NA
3	0.066	1yvjA	0.465	3.89	0.110	0.558	2.7.10.2	NA
4	0.066	3eyhA	0.454	4.09	0.087	0.549	2.7.10.2	NA
5	0.066	1ql6A	0.461	4.43	0.075	0.570	2.7.11.19 2.7.1.38	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	0.11	2nryA	0.461	3.97	0.109	0.558	0.21	STU	complex1.pdb.gz	208,209,214,233,234,236
2	0.10	2oidD	0.443	3.97	0.109	0.535	0.19	ANP	complex2.pdb.gz	209,234,236
3	0.10	2h96B	0.461	4.42	0.100	0.577	0.23	893	complex3.pdb.gz	205,207,235,239
4	0.09	3kvxA	0.437	4.53	0.093	0.549	0.18	FMY	complex4.pdb.gz	205,206,207,209,233,236
5	0.09	3oxiA	0.427	4.65	0.106	0.542	0.27	SYY	complex5.pdb.gz	230,231,232,233,235,236
6	0.09	1pmnA	0.434	4.66	0.083	0.556	0.16	984	complex6.pdb.gz	208,209,234,235
7	0.09	3eljA	0.438	4.65	0.092	0.558	0.14	GS7	complex7.pdb.gz	218,234,235,236
8	0.08	2nryD	0.457	3.89	0.107	0.549	0.19	STU	complex8.pdb.gz	230,231,232,236
9	0.07	2gmxA	0.462	4.29	0.093	0.572	0.18	877	complex9.pdb.gz	233,240,241,242
10	0.07	3fbvE	0.459	4.52	0.089	0.572	0.16	APJ	complex10.pdb.gz	230,231,233,235

	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.