D-I-TASSER P40925

D-I-TASSER results for P40925

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

Summary of the Protein

Uniprot ID: P40925
Protein Name: Malate dehydrogenase, cytoplasmic
Gene Name: MDH1

Input Sequence in FASTA format

>P40925 (334 residues)
MSEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDC
ALPLLKDVIATDKEDVAFKDLDVAILVGSMPRREGMERKDLLKANVKIFKSQGAALDKYA
KKSVKVIVVGNPANTNCLTASKSAPSIPKENFSCLTRLDHNRAKAQIALKLGVTANDVKN
VIIWGNHSSTQYPDVNHAKVKLQGKEVGVYEALKDDSWLKGEFVTTVQQRGAAVIKARKL
SSAMSAAKAICDHVRDIWFGTPEGEFVSMGVISDGNSYGVPDDLLYSFPVVIKNKTWKFV
EGLPINDFSREKMDLTAKELTEEKESAFEFLSSA

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	P40925-D1	1-153	153		MSEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEDVAFKDLDVAILVGSMPRREGMERKDLLKANVKIFKSQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKENFS
2	P40925-D2	154-334	181		CLTRLDHNRAKAQIALKLGVTANDVKNVIIWGNHSSTQYPDVNHAKVKLQGKEVGVYEALKDDSWLKGEFVTTVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGVISDGNSYGVPDDLLYSFPVVIKNKTWKFVEGLPINDFSREKMDLTAKELTEEKESAFEFLSSA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.968

(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	4mdhA	0.97	1.20	0.940	0.994	model1_4mdhA.pdb.gz
2	5nufA	0.97	0.97	0.613	0.991	model1_5nufA.pdb.gz
3	7mdhB	0.95	1.45	0.442	0.988	model1_7mdhB.pdb.gz
4	1wziA	0.95	1.26	0.538	0.979	model1_1wziA.pdb.gz
5	4uulA	0.95	1.47	0.429	0.991	model1_4uulA.pdb.gz
6	3d5tC	0.95	0.96	0.545	0.967	model1_3d5tC.pdb.gz
7	4tvoA	0.95	1.59	0.506	0.979	model1_4tvoA.pdb.gz
8	6pblA	0.95	1.41	0.468	0.979	model1_6pblA.pdb.gz
9	4uuoA	0.94	1.21	0.489	0.967	model1_4uuoA.pdb.gz
10	6um4A	0.94	1.51	0.472	0.970	model1_6um4A.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	0.94	catalytic activity
GO:0016491	0.93	oxidoreductase activity
GO:0016614	0.89	oxidoreductase activity, acting on CH-OH group of donors
GO:0016615	0.74	malate dehydrogenase activity
GO:0016616	0.73	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0030060	0.59	L-malate dehydrogenase 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:0044699	0.90	single-organism process
GO:0009987	0.85	cellular process
GO:0008152	0.84	metabolic process
GO:0044763	0.80	single-organism cellular process
GO:0044710	0.78	single-organism metabolic process
GO:0044281	0.75	small molecule metabolic process
GO:0071704	0.73	organic substance metabolic process
GO:0044237	0.65	cellular metabolic process
GO:0044238	0.59	primary metabolic process
GO:0006082	0.53	organic 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:0044464	0.99	cell part
GO:0044424	0.98	intracellular part
GO:0044444	0.89	cytoplasmic part
GO:0043226	0.77	organelle
GO:0043229	0.72	intracellular organelle
GO:0043227	0.68	membrane-bounded organelle
GO:0044422	0.57	organelle part
GO:0043231	0.57	intracellular membrane-bounded organelle
GO:0044446	0.56	intracellular organelle part
GO:0005829	0.52	cytosol

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	0.700	1iz9A	0.954	1.22	0.544	0.979	1.1.1.37	87,131,158,162,187,189,229,232,241,243,246
2	0.477	2mdhA	0.948	1.10	0.444	0.970	1.1.1.37	187
3	0.385	2mdhB	0.947	1.16	0.321	0.970	1.1.1.37	11,106,187,246
4	0.380	1gv1A	0.820	2.20	0.237	0.898	1.1.1.37	91,129,131,185,187,232
5	0.292	2j5rA	0.807	2.22	0.189	0.886	1.1.1.37	157,162,239

	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	0.95	5mdhA	0.979	1.24	0.955	0.997	1.84	NAD	complex1.pdb.gz	11,13,14,15,16,42,87,88,89,90,91,108,129,130,131,155,187,241,242,246
2	0.47	5mdhA	0.979	1.24	0.955	0.997	1.30	MAK	complex2.pdb.gz	131,158,187,235,242
3	0.37	1v6aB	0.823	2.57	0.201	0.922	1.34	TRE	complex3.pdb.gz	14,42,43,49,88,89,91
4	0.33	1bdm0	0.925	1.20	0.539	0.949	1.64	III	complex4.pdb.gz	18,22,23,26,28,32,48,49,52,55,56,58,59,60,61,62,161,162,165,169,175,230,233,234,237,238,242,243,244,245,248
5	0.15	1smkC	0.818	2.52	0.228	0.904	1.00	CIT	complex5.pdb.gz	16,92,131,158,187,231,235,241,242,246

	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.