D-I-TASSER P67809

D-I-TASSER results for P67809

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

Summary of the Protein

Uniprot ID: P67809
Protein Name: Y-box-binding protein 1
Gene Name: YBX1

Input Sequence in FASTA format

>P67809 (324 residues)
MSSEAETQQPPAAPPAAPALSAADTKPGTTGSGAGSGGPGGLTSAAPAGGDKKVIATKVL
GTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGA
EAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEG
QAQQRRPYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRG
YRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDG
KETKAADPPAENSSAPEAEQGGAE

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	P67809-D1	1-324	324		MSSEAETQQPPAAPPAAPALSAADTKPGTTGSGAGSGGPGGLTSAAPAGGDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVMEGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAPEAEQGGAE

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.4011

(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	5i2tA	0.82	3.18	0.054	0.972	model1_5i2tA.pdb.gz
2	5wlcLO	0.80	3.51	0.066	0.978	model1_5wlcLO.pdb.gz
3	5oqlA	0.80	3.54	0.069	0.978	model1_5oqlA.pdb.gz
4	5teeA	0.76	3.68	0.064	0.951	model1_5teeA.pdb.gz
5	1pevA	0.76	3.93	0.055	0.944	model1_1pevA.pdb.gz
6	4xfvA	0.76	3.70	0.069	0.938	model1_4xfvA.pdb.gz
7	5wyjBE	0.74	4.10	0.061	0.935	model1_5wyjBE.pdb.gz
8	2ymuA	0.74	3.66	0.067	0.914	model1_2ymuA.pdb.gz
9	5oqlO	0.74	4.25	0.051	0.951	model1_5oqlO.pdb.gz
10	4nsxA	0.73	4.20	0.058	0.935	model1_4nsxA.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:1901363	0.98	heterocyclic compound binding
GO:0097159	0.98	organic cyclic compound binding
GO:0003676	0.97	nucleic acid binding
GO:0003723	0.92	RNA 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:0065007	0.87	biological regulation
GO:0050789	0.86	regulation of biological process
GO:0060255	0.84	regulation of macromolecule metabolic process
GO:0010468	0.82	regulation of gene expression
GO:0050794	0.76	regulation of cellular process
GO:0080090	0.73	regulation of primary metabolic process
GO:0031323	0.73	regulation of cellular metabolic process
GO:0051171	0.72	regulation of nitrogen compound metabolic process
GO:0031326	0.72	regulation of cellular biosynthetic process
GO:0010556	0.72	regulation of macromolecule biosynthetic process
GO:0009987	0.72	cellular process
GO:2000112	0.71	regulation of cellular macromolecule biosynthetic process
GO:0010608	0.66	posttranscriptional regulation of gene expression
GO:0019219	0.65	regulation of nucleobase-containing compound metabolic process
GO:0051252	0.64	regulation of RNA metabolic process
GO:0048519	0.58	negative regulation of biological process
GO:0048523	0.57	negative regulation of cellular process
GO:0008152	0.54	metabolic process
GO:0010605	0.53	negative regulation of macromolecule metabolic process
GO:0071704	0.52	organic substance metabolic process
GO:0051172	0.52	negative regulation of nitrogen compound metabolic process
GO:0031324	0.52	negative regulation of cellular metabolic process
GO:0010629	0.52	negative regulation of gene expression
GO:0031327	0.51	negative regulation of cellular biosynthetic process
GO:2000113	0.50	negative regulation of cellular macromolecule biosynthetic process
GO:0045934	0.50	negative regulation of nucleobase-containing compound metabolic process
GO:0044237	0.50	cellular metabolic process
GO:0043170	0.50	macromolecule 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:0044424	1.00	intracellular part
GO:0032991	0.77	macromolecular complex
GO:0043226	0.76	organelle
GO:0043229	0.75	intracellular organelle
GO:0044446	0.72	intracellular organelle part
GO:0030529	0.72	intracellular ribonucleoprotein complex
GO:0044428	0.67	nuclear part
GO:0044444	0.66	cytoplasmic part
GO:0043227	0.62	membrane-bounded organelle
GO:0043231	0.60	intracellular membrane-bounded organelle
GO:0005634	0.51	nucleus

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	0.097	3dr2A	0.572	3.98	0.038	0.728	3.1.1.17	NA
2	0.068	1rwlA	0.573	4.03	0.049	0.732	2.7.11.1	108
3	0.067	1ri6A	0.615	3.64	0.058	0.756	3.1.1.31	NA
4	0.067	1jofA	0.634	3.68	0.050	0.784	5.5.1.5	NA
5	0.067	2h47H	0.631	3.76	0.056	0.787	1.4.99.4	101,128

	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	0.02	2xl2B	0.682	3.50	0.050	0.827	0.61	III	complex1.pdb.gz	168,208,209,210,212,213,253,259,275
2	0.02	2h6qA	0.682	3.52	0.050	0.827	0.48	III	complex2.pdb.gz	53,55,68,99,113,125,176,218,248,249,250,252,294
3	0.02	1gg20	0.673	3.53	0.050	0.821	0.47	III	complex3.pdb.gz	78,79,193,227,229,230,231,257,258,259,275,300,301,302,303,304
4	0.02	3ijeA	0.698	3.55	0.059	0.852	0.49	UUU	complex4.pdb.gz	116,124,133,134
5	0.02	2xl2A	0.682	3.50	0.050	0.827	0.52	III	complex5.pdb.gz	60,104,105,107,108,146
6	0.02	2bcj5	0.674	3.52	0.047	0.821	0.56	III	complex6.pdb.gz	51,53,69,70,71,93,97,114,161
7	0.02	2xl3B	0.682	3.51	0.050	0.827	0.46	III	complex7.pdb.gz	104,127,130,186
8	0.01	2i3s0	0.668	3.68	0.055	0.824	0.41	III	complex8.pdb.gz	50,51,69,159,201,203,242,247
9	0.01	2trc0	0.675	3.50	0.050	0.821	0.41	III	complex9.pdb.gz	98,136,162,203,247,250,284,285
10	0.01	2abz3	0.090	3.90	0.071	0.114	0.43	III	complex10.pdb.gz	100,102,104,109

	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.