D-I-TASSER Q5JVF3

D-I-TASSER results for Q5JVF3

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

Summary of the Protein

Uniprot ID: Q5JVF3
Protein Name: PCI domain-containing protein 2
Gene Name: PCID2

Input Sequence in FASTA format

>Q5JVF3 (399 residues)
MAHITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEPPYDE
MFAAHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLRVFAN
NADQQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRAGIEDSKKWGMLFLVNQLFKIYF
KINKLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHC
HRSSQKNKRMILIYLLPVKMLLGHMPTVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAK
HEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEV
QCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC

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	Q5JVF3-D1	1-158	158		MAHITINQYLQQVYEAIDSRDGASCAELVSFKHPHVANPRLQMASPEEKCQQVLEPPYDEMFAAHLRCTYAVGNHDFIEAYKCQTVIVQSFLRAFQAHKEENWALPVMYAVALDLRVFANNADQQLVKKGKSKVGDMLEKAAELLMSCFRVCASDTRA
2	Q5JVF3-D2	159-266	108		GIEDSKKWGMLFLVNQLFKIYFKINKLHLCKPLIRAIDSSNLKDDYSTAQRVTYKYYVGRKAMFDSDFKQAEEYLSFAFEHCHRSSQKNKRMILIYLLPVKMLLGHMP
3	Q5JVF3-D3	267-399	133		TVELLKKYHLMQFAEVTRAVSEGNLLLLHEALAKHEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVDIDEVQCILANLIYMGHVKGYISHQHQKLVVSKQNPFPPLSTVC

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.84

(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	3t5vB	0.74	4.42	0.196	0.952	model1_3t5vB.pdb.gz
2	5mpbS	0.68	4.69	0.084	0.885	model1_5mpbS.pdb.gz
3	3jckA	0.68	3.68	0.122	0.817	model1_3jckA.pdb.gz
4	3txmA	0.65	4.43	0.116	0.825	model1_3txmA.pdb.gz
5	5l4kS	0.65	3.96	0.155	0.792	model1_5l4kS.pdb.gz
6	5l4kQ	0.64	4.91	0.122	0.835	model1_5l4kQ.pdb.gz
7	4d10B	0.63	3.92	0.114	0.767	model1_4d10B.pdb.gz
8	6fec2	0.62	5.35	0.084	0.867	model1_6fec2.pdb.gz
9	6vp9B	0.61	4.92	0.122	0.842	model1_6vp9B.pdb.gz
10	4u1cC	0.61	4.94	0.091	0.822	model1_4u1cC.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	0.67	heterocyclic compound binding
GO:0097159	0.67	organic cyclic compound binding
GO:0003676	0.60	nucleic acid binding
GO:0003824	0.51	catalytic 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:0050794	0.77	regulation of cellular process
GO:0044699	0.72	single-organism process
GO:0048856	0.67	anatomical structure development
GO:0044767	0.67	single-organism developmental process
GO:0009987	0.67	cellular process
GO:0080090	0.62	regulation of primary metabolic process
GO:0060255	0.62	regulation of macromolecule metabolic process
GO:0031323	0.62	regulation of cellular metabolic process
GO:0048522	0.61	positive regulation of cellular process
GO:0031326	0.61	regulation of cellular biosynthetic process
GO:2001141	0.60	regulation of RNA biosynthetic process
GO:2000112	0.60	regulation of cellular macromolecule biosynthetic process
GO:0051726	0.60	regulation of cell cycle
GO:0048523	0.60	negative regulation of cellular process
GO:0032268	0.60	regulation of cellular protein metabolic process
GO:0031325	0.60	positive regulation of cellular metabolic process
GO:0010468	0.60	regulation of gene expression
GO:1901990	0.59	regulation of mitotic cell cycle phase transition
GO:0065008	0.59	regulation of biological quality
GO:0051128	0.59	regulation of cellular component organization
GO:0050790	0.59	regulation of catalytic activity
GO:0045893	0.59	positive regulation of transcription, DNA-templated
GO:0044092	0.59	negative regulation of molecular function
GO:0032269	0.59	negative regulation of cellular protein metabolic process
GO:0010608	0.59	posttranscriptional regulation of gene expression
GO:2000117	0.58	negative regulation of cysteine-type endopeptidase activity
GO:0090267	0.58	positive regulation of mitotic cell cycle spindle assembly checkpoint
GO:0048536	0.58	spleen development
GO:0043488	0.58	regulation of mRNA stability
GO:0043066	0.58	negative regulation of apoptotic process
GO:0008152	0.53	metabolic process
GO:0071704	0.51	organic substance metabolic process
GO:0044238	0.50	primary 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	0.94	macromolecular complex
GO:0043234	0.86	protein complex
GO:0043226	0.78	organelle
GO:0043229	0.77	intracellular organelle
GO:0043231	0.71	intracellular membrane-bounded organelle
GO:0044422	0.70	organelle part
GO:0044446	0.69	intracellular organelle part
GO:0005634	0.69	nucleus
GO:0044444	0.60	cytoplasmic part
GO:0044428	0.57	nuclear part
GO:0008541	0.53	proteasome regulatory particle, lid subcomplex
GO:0005737	0.53	cytoplasm

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	3ebgA	0.412	6.15	0.047	0.632	3.4.11.-	NA
2	0.060	2vn7A	0.393	5.98	0.034	0.599	3.2.1.3	NA
3	0.060	1s0kA	0.376	6.82	0.066	0.622	3.2.1.18	NA
4	0.060	1ofdA	0.393	7.08	0.056	0.662	1.4.7.1	NA
5	0.060	2dqmA	0.401	6.30	0.038	0.624	3.4.11.2	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	0.01	2bptA	0.486	5.04	0.068	0.659	0.71	III	complex1.pdb.gz	218,221,222,225,258,261
2	0.01	2gl7D	0.482	6.22	0.064	0.749	0.68	III	complex2.pdb.gz	229,253,257,261
3	0.01	1f59A	0.448	5.64	0.073	0.639	0.54	III	complex3.pdb.gz	214,217,218,221,222,258,262

	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.