D-I-TASSER O75874

D-I-TASSER results for O75874

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

Summary of the Protein

Uniprot ID: O75874
Protein Name: Isocitrate dehydrogenase [NADP] cytoplasmic
Gene Name: IDH1

Input Sequence in FASTA format

>O75874 (414 residues)
MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDA
AEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILGGTVFREAIICKNIPRL
VSGWVKPIIIGRHAYGDQYRATDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAM
GMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFE
AQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDG
KTVEAEAAHGTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALE
EVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL

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	O75874-D1	1-104	104		MSKKISGGSVVEMQGDEMTRIIWELIKEKLIFPYVELDLHSYDLGIENRDATNDQVTKDAAEAIKKHNVGVKCATITPDEKRVEEFKLKQMWKSPNGTIRNILG
2	O75874-D2	105-141,182-309	165		GTVFREAIICKNIPRLVSGWVKPIIIGRHAYGDQYRAMYNQDKSIEDFAHSSFQMALSKGWPLYLSTKNTILKKYDGRFKDIFQEIYDKQYKSQFEAQKIWYEHRLIDDMVAQAMKSEGGFIWACKNYDGDVQSDSVAQGYGSLGMMTSVLVCPDGKTVEAEAAH
3	O75874-D3	142-181	40		TDFVVPGPGKVEITYTPSDGTQKVTYLVHNFEEGGGVAMG
4	O75874-D4	310-414	105		GTVTRHYRMYQKGQETSTNPIASIFAWTRGLAHRAKLDNNKELAFFANALEEVSIETIEAGFMTKDLAACIKGLPNVQRSDYLNTFEFMDKLGENLKIKLAQAKL

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.87

(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	1lwdA	0.97	1.13	0.658	0.988	model1_1lwdA.pdb.gz
2	2qfwD	0.95	1.27	0.620	0.978	model1_2qfwD.pdb.gz
3	3us8A	0.92	1.27	0.655	0.944	model1_3us8A.pdb.gz
4	2uxrA	0.92	1.94	0.480	0.966	model1_2uxrA.pdb.gz
5	6lkzC	0.88	2.29	0.308	0.954	model1_6lkzC.pdb.gz
6	6ixlA	0.85	2.42	0.309	0.937	model1_6ixlA.pdb.gz
7	1zorA	0.84	3.16	0.494	0.954	model1_1zorA.pdb.gz
8	1itwA	0.83	2.59	0.100	0.920	model1_1itwA.pdb.gz
9	4zdaA	0.83	2.52	0.121	0.915	model1_4zdaA.pdb.gz
10	1t09A	0.83	3.69	0.897	0.983	model1_1t09A.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:0004448	1.00	isocitrate dehydrogenase activity
GO:0004450	0.97	isocitrate dehydrogenase (NADP+) activity
GO:0046872	0.70	metal ion binding
GO:0000287	0.62	magnesium ion 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:0044699	0.99	single-organism process
GO:0008152	0.93	metabolic process
GO:0009987	0.90	cellular process
GO:0071704	0.89	organic substance metabolic process
GO:0044710	0.89	single-organism metabolic process
GO:0044281	0.88	small molecule metabolic process
GO:0044237	0.88	cellular metabolic process
GO:0044763	0.87	single-organism cellular process
GO:0006082	0.84	organic acid metabolic process
GO:0019752	0.82	carboxylic acid metabolic process
GO:0006102	0.75	isocitrate metabolic process
GO:0043648	0.53	dicarboxylic acid metabolic process
GO:0044238	0.50	primary metabolic process
GO:0006103	0.50	2-oxoglutarate 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:0044464	1.00	cell part
GO:0044424	0.99	intracellular part
GO:0044444	0.98	cytoplasmic part
GO:0043226	0.88	organelle
GO:0043229	0.87	intracellular organelle
GO:0043227	0.87	membrane-bounded organelle
GO:0043231	0.86	intracellular membrane-bounded organelle
GO:0005739	0.63	mitochondrion

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	0.769	1lwdA	0.968	1.13	0.658	0.988	1.1.1.42	212,252
2	0.506	1x0lA	0.710	2.86	0.178	0.799	1.1.1.87	212,252
3	0.505	2dhtA	0.731	3.49	0.191	0.860	1.1.1.42	212,252
4	0.498	1hqsA	0.793	2.87	0.178	0.884	1.1.1.42	212,252
5	0.489	1xgvA	0.765	3.44	0.176	0.891	1.1.1.42	212,252

	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	0.96	1t0lA	0.945	1.79	0.959	0.993	1.65	NAP	complex1.pdb.gz	72,74,75,76,77,82,96,288,308,309,310,311,312,313,314,315,327,328
2	0.28	1ideA	0.786	2.91	0.166	0.879	0.83	NAP	complex2.pdb.gz	18,76,96,307,308,309,310,312,313,327,328,374,375
3	0.11	2qfxC	0.945	1.45	0.632	0.978	1.18	AKG	complex3.pdb.gz	77,94,96,100

	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.