D-I-TASSER Q07002

D-I-TASSER results for Q07002

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

Summary of the Protein

Uniprot ID: Q07002
Protein Name: Cyclin-dependent kinase 18
Gene Name: CDK18

Input Sequence in FASTA format

>Q07002 (474 residues)
MIMNKMKNFKRRFSLSVPRTETIEESLAEFTEQFNQLHNRRNENLQLGPLGRDPPQECST
FSPTDSGEEPGQLSPGVQFQRRQNQRRFSMEDVSKRLSLPMDIRLPQEFLQKLQMESPDL
PKPLSRMSRRASLSDIGFGKLETYVKLDKLGEGTYATVFKGRSKLTENLVALKEIRLEHE
EGAPCTAIREVSLLKNLKHANIVTLHDLIHTDRSLTLVFEYLDSDLKQYLDHCGNLMSMH
NVKIFMFQLLRGLAYCHHRKILHRDLKPQNLLINERGELKLADFGLARAKSVPTKTYSNE
VVTLWYRPPDVLLGSTEYSTPIDMWGVGCIHYEMATGRPLFPGSTVKEELHLIFRLLGTP
TEETWPGVTAFSEFRTYSFPCYLPQPLINHAPRLDTDGIHLLSSLLLYESKSRMSAEAAL
SHSYFRSLGERVHQLEDTASIFSLKEIQLQKDPGYRGLAFQQPGRGKNRRQSIF

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	Q07002-D1	1-97	97		MIMNKMKNFKRRFSLSVPRTETIEESLAEFTEQFNQLHNRRNENLQLGPLGRDPPQECSTFSPTDSGEEPGQLSPGVQFQRRQNQRRFSMEDVSKRL
2	Q07002-D2	98-220	123		SLPMDIRLPQEFLQKLQMESPDLPKPLSRMSRRASLSDIGFGKLETYVKLDKLGEGTYATVFKGRSKLTENLVALKEIRLEHEEGAPCTAIREVSLLKNLKHANIVTLHDLIHTDRSLTLVFE
3	Q07002-D3	221-474	254		YLDSDLKQYLDHCGNLMSMHNVKIFMFQLLRGLAYCHHRKILHRDLKPQNLLINERGELKLADFGLARAKSVPTKTYSNEVVTLWYRPPDVLLGSTEYSTPIDMWGVGCIHYEMATGRPLFPGSTVKEELHLIFRLLGTPTEETWPGVTAFSEFRTYSFPCYLPQPLINHAPRLDTDGIHLLSSLLLYESKSRMSAEAALSHSYFRSLGERVHQLEDTASIFSLKEIQLQKDPGYRGLAFQQPGRGKNRRQSIF

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.63

(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	3i4bA	0.64	2.62	0.271	0.686	model1_3i4bA.pdb.gz
2	4e7wA	0.63	2.98	0.280	0.688	model1_4e7wA.pdb.gz
3	3eb0A	0.60	2.43	0.295	0.635	model1_3eb0A.pdb.gz
4	7nxjA	0.60	2.32	0.362	0.635	model1_7nxjA.pdb.gz
5	6z3uB	0.59	2.70	0.327	0.643	model1_6z3uB.pdb.gz
6	3e3pA	0.59	2.83	0.270	0.648	model1_3e3pA.pdb.gz
7	1unlA	0.59	1.52	0.557	0.610	model1_1unlA.pdb.gz
8	5z33A	0.59	2.68	0.300	0.635	model1_5z33A.pdb.gz
9	7kpvA	0.59	2.74	0.284	0.639	model1_7kpvA.pdb.gz
10	6gubA	0.59	1.73	0.531	0.612	model1_6gubA.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:0004672	0.98	protein kinase activity
GO:0004674	0.93	protein serine/threonine kinase activity
GO:1901363	0.84	heterocyclic compound binding
GO:0097159	0.84	organic cyclic compound binding
GO:0035639	0.78	purine ribonucleoside triphosphate binding
GO:0032555	0.78	purine ribonucleotide binding
GO:0032550	0.78	purine ribonucleoside binding
GO:0005524	0.76	ATP binding
GO:0004693	0.51	cyclin-dependent protein serine/threonine kinase activity

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	0.95	cellular process
GO:0071704	0.89	organic substance metabolic process
GO:0065007	0.89	biological regulation
GO:0044237	0.89	cellular metabolic process
GO:0050789	0.88	regulation of biological process
GO:0044260	0.88	cellular macromolecule metabolic process
GO:0044238	0.88	primary metabolic process
GO:0050794	0.87	regulation of cellular process
GO:0006796	0.84	phosphate-containing compound metabolic process
GO:0006464	0.84	cellular protein modification process
GO:0006468	0.83	protein phosphorylation
GO:0007165	0.75	signal transduction
GO:0044699	0.67	single-organism process
GO:0035556	0.65	intracellular signal transduction
GO:0044763	0.60	single-organism cellular process
GO:0018193	0.56	peptidyl-amino acid modification
GO:0050896	0.54	response to stimulus
GO:0048518	0.53	positive regulation of biological process
GO:1901360	0.51	organic cyclic compound metabolic process
GO:0046483	0.51	heterocycle metabolic process
GO:0034641	0.51	cellular nitrogen compound metabolic process
GO:0019222	0.51	regulation of metabolic process
GO:0018105	0.51	peptidyl-serine phosphorylation
GO:0006725	0.51	cellular aromatic compound metabolic process
GO:0090304	0.50	nucleic acid metabolic process
GO:0080090	0.50	regulation of primary metabolic process
GO:0060255	0.50	regulation of macromolecule metabolic process
GO:0031323	0.50	regulation of cellular metabolic process
GO:0006950	0.50	response to stress

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:0044464	1.00	cell part
GO:0044424	0.97	intracellular part
GO:0043226	0.80	organelle
GO:0043229	0.78	intracellular organelle
GO:0043227	0.75	membrane-bounded organelle
GO:0005737	0.74	cytoplasm
GO:0043231	0.73	intracellular membrane-bounded organelle
GO:0005634	0.66	nucleus
GO:0044444	0.55	cytoplasmic part
GO:0016020	0.55	membrane

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	0.298	2bfyB	0.528	2.65	0.268	0.574	2.7.11.1	150,173,227,272
2	0.234	3mtlA	0.557	2.79	0.691	0.606	2.7.11.22	151,153,155,158,262,264,266,269,282,284,286,303,307,322
3	0.142	1vywA	0.595	1.92	0.512	0.622	2.7.11.22 2.7.1.37	NA
4	0.125	3blrA	0.584	2.40	0.395	0.625	2.7.11.23 2.7.11.22	NA
5	0.124	2pk9A	0.569	1.77	0.530	0.593	2.7.11.22	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	0.76	3o0gB	0.539	1.40	0.559	0.555	1.55	3O0	complex1.pdb.gz	150,158,171,173,203,220,221,222,223,224,228,272,283
2	0.69	1ungB	0.547	1.38	0.566	0.563	0.91	ALH	complex2.pdb.gz	171,220,222,223,272,282
3	0.67	3miaA	0.597	2.59	0.374	0.641	0.92	ANP	complex3.pdb.gz	171,173,219,220,222,269,270,272,283
4	0.63	1q3dB	0.623	2.51	0.281	0.669	1.27	STU	complex4.pdb.gz	150,151,153,158,174,220,221,222,269,272,282,283
5	0.63	3f88B	0.632	2.45	0.277	0.677	1.18	3HT	complex5.pdb.gz	150,154,157,172,174,219,220,221,222,223,225,228,271,282,283
6	0.62	3i4bA	0.636	2.62	0.271	0.686	1.35	Z48	complex6.pdb.gz	152,153,154,156,158,171,173,219,220,222,223,228,270,272,282,283
7	0.60	3f88A	0.632	2.46	0.277	0.677	1.20	2HT	complex7.pdb.gz	151,158,269,270,283
8	0.59	3ngaA	0.580	2.09	0.241	0.614	1.30	3NG	complex8.pdb.gz	150,151,152,158,171,173,203,219,220,269,282,283
9	0.38	2ow3A	0.630	2.82	0.277	0.686	1.27	BIM	complex9.pdb.gz	172,220,221,222,223,225,269,272,282,283
10	0.32	3mb6A	0.578	1.91	0.251	0.608	1.17	01I	complex10.pdb.gz	150,158,171,173,219,271,282,283

	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.