D-I-TASSER P39905

D-I-TASSER results for P39905

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

Summary of the Protein

Uniprot ID: P39905
Protein Name: Glial cell line-derived neurotrophic factor
Gene Name: GDNF

Input Sequence in FASTA format

>P39905 (211 residues)
MKLWDVVAVCLVLLHTASAFPLPAGKRPPEAPAEDRSLGRRRAPFALSSDSNMPEDYPDQ
FDDVMDFIQATIKRLKRSPDKQMAVLPRRERNRQAAAANPENSRGKGRRGQRGKNRGCVL
TAIHLNVTDLGLGYETKEELIFRYCSGSCDAAETTYDKILKNLSRNRRLVSDKVGQACCR
PIAFDDDLSFLDDNLVYHILRKHSAKRCGCI

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	P39905-D1	1-211	211		MKLWDVVAVCLVLLHTASAFPLPAGKRPPEAPAEDRSLGRRRAPFALSSDSNMPEDYPDQFDDVMDFIQATIKRLKRSPDKQMAVLPRRERNRQAAAANPENSRGKGRRGQRGKNRGCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCDAAETTYDKILKNLSRNRRLVSDKVGQACCRPIAFDDDLSFLDDNLVYHILRKHSAKRCGCI

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.552

(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	6r9tA	0.44	5.36	0.046	0.725	model1_6r9tA.pdb.gz
2	3kvnX	0.43	5.94	0.036	0.768	model1_3kvnX.pdb.gz
3	3fubD	0.42	1.96	0.857	0.465	model1_3fubD.pdb.gz
4	6xmpA	0.42	5.52	0.032	0.692	model1_6xmpA.pdb.gz
5	5xsyA	0.42	6.31	0.045	0.815	model1_5xsyA.pdb.gz
6	5u1sA	0.41	5.23	0.043	0.654	model1_5u1sA.pdb.gz
7	6d4hA	0.41	5.78	0.095	0.716	model1_6d4hA.pdb.gz
8	6i7dA	0.41	5.63	0.027	0.697	model1_6i7dA.pdb.gz
9	1st6A	0.41	5.65	0.053	0.692	model1_1st6A.pdb.gz
10	6bfiA	0.41	5.67	0.050	0.682	model1_6bfiA.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:0005102	0.84	receptor binding
GO:0042802	0.69	identical protein binding
GO:0042803	0.68	protein homodimerization 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	0.98	single-organism process
GO:0032502	0.98	developmental process
GO:0044767	0.91	single-organism developmental process
GO:0065007	0.85	biological regulation
GO:0050789	0.84	regulation of biological process
GO:0050794	0.83	regulation of cellular process
GO:0009987	0.82	cellular process
GO:0009653	0.81	anatomical structure morphogenesis
GO:0044763	0.79	single-organism cellular process
GO:0048856	0.76	anatomical structure development
GO:0048518	0.70	positive regulation of biological process
GO:0080090	0.67	regulation of primary metabolic process
GO:0048522	0.67	positive regulation of cellular process
GO:0031323	0.67	regulation of cellular metabolic process
GO:0060255	0.66	regulation of macromolecule metabolic process
GO:0048731	0.65	system development
GO:0031325	0.65	positive regulation of cellular metabolic process
GO:0010604	0.65	positive regulation of macromolecule metabolic process
GO:0023051	0.64	regulation of signaling
GO:0010646	0.64	regulation of cell communication
GO:0031326	0.63	regulation of cellular biosynthetic process
GO:0019219	0.63	regulation of nucleobase-containing compound metabolic process
GO:0006928	0.63	movement of cell or subcellular component
GO:0042981	0.62	regulation of apoptotic process
GO:0016477	0.62	cell migration
GO:0006355	0.62	regulation of transcription, DNA-templated
GO:0016043	0.61	cellular component organization
GO:0032501	0.60	multicellular organismal process
GO:0006357	0.60	regulation of transcription from RNA polymerase II promoter
GO:0048729	0.59	tissue morphogenesis
GO:0044707	0.59	single-multicellular organism process
GO:0031175	0.59	neuron projection development
GO:0001755	0.59	neural crest cell migration
GO:0048523	0.58	negative regulation of cellular process
GO:0065008	0.57	regulation of biological quality
GO:0051239	0.57	regulation of multicellular organismal process
GO:0045893	0.57	positive regulation of transcription, DNA-templated
GO:0001658	0.57	branching involved in ureteric bud morphogenesis
GO:2000026	0.56	regulation of multicellular organismal development
GO:0065009	0.56	regulation of molecular function
GO:0051240	0.56	positive regulation of multicellular organismal process
GO:2000027	0.55	regulation of organ morphogenesis
GO:0060688	0.55	regulation of morphogenesis of a branching structure
GO:0051094	0.55	positive regulation of developmental process
GO:0051049	0.55	regulation of transport
GO:0050804	0.55	modulation of synaptic transmission
GO:0048513	0.55	animal organ development
GO:0045944	0.55	positive regulation of transcription from RNA polymerase II promoter
GO:0043085	0.55	positive regulation of catalytic activity
GO:0043069	0.55	negative regulation of programmed cell death
GO:0010608	0.55	posttranscriptional regulation of gene expression
GO:0003008	0.55	system process
GO:0090190	0.54	positive regulation of branching involved in ureteric bud morphogenesis
GO:0072107	0.54	positive regulation of ureteric bud formation
GO:0051584	0.54	regulation of dopamine uptake involved in synaptic transmission
GO:0048485	0.54	sympathetic nervous system development
GO:0048484	0.54	enteric nervous system development
GO:0048255	0.54	mRNA stabilization
GO:0043524	0.54	negative regulation of neuron apoptotic process
GO:0032770	0.54	positive regulation of monooxygenase activity
GO:0030432	0.54	peristalsis
GO:0021784	0.54	postganglionic parasympathetic fiber development
GO:0001656	0.54	metanephros development
GO:0007165	0.51	signal transduction

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:0005576	0.82	extracellular region
GO:0044464	0.71	cell part
GO:0044424	0.53	intracellular part

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	1ofdA	0.317	6.43	0.019	0.611	1.4.7.1	NA
2	0.060	3kvnX	0.429	5.94	0.036	0.768	3.1.1.1	3,181
3	0.060	2vdcA	0.403	5.83	0.033	0.701	1.4.1.13	NA
4	0.060	3kzwA	0.377	5.30	0.048	0.621	3.4.11.1	NA
5	0.060	2f89F	0.385	5.08	0.021	0.611	2.5.1.1 2.5.1.10	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.35	2v5e0	0.382	2.51	0.827	0.431	1.45	III	complex1.pdb.gz	125,129,130,131,132,142,144,145,175,176,177,178,180,181,203,211
	2	0.01	6r1rA	0.398	5.86	0.054	0.692	0.54	III	complex2.pdb.gz	160,161,162,163,164

	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.