D-I-TASSER P54317

D-I-TASSER results for P54317

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

Summary of the Protein

Uniprot ID: P54317
Protein Name: Pancreatic lipase-related protein 2
Gene Name: PNLIPRP2

Input Sequence in FASTA format

>P54317 (469 residues)
MLPPWTLGLLLLATVRGKEVCYGQLGCFSDEKPWAGTLQRPVKLLPWSPEDIDTRFLLYT
NENPNNFQLITGTEPDTIEASNFQLDRKTRFIIHGFLDKAEDSWPSDMCKKMFEVEKVNC
ICVDWRHGSRAMYTQAVQNIRVVGAETAFLIQALSTQLGYSLEDVHVIGHSLGAHTAAEA
GRRLGGRVGRITGLDPAGPCFQDEPEEVRLDPSDAVFVDVIHTDSSPIVPSLGFGMSQKV
GHLDFFPNGGKEMPGCKKNVLSTITDIDGIWEGIGGFVSCNHLRSFEYYSSSVLNPDGFL
GYPCASYDEFQESKCFPCPAEGCPKMGHYADQFKGKTSAVEQTFFLNTGESGNFTSWRYK
ISVTLSGKEKVNGYIRIALYGSNENSKQYEIFKGSLKPDASHTCAIDVDFNVGKIQKVKF
LWNKRGINLSEPKLGASQITVQSGEDGTEYNFCSSDTVEENVLQSLYPC

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	P54317-D1	1-355	355		MLPPWTLGLLLLATVRGKEVCYGQLGCFSDEKPWAGTLQRPVKLLPWSPEDIDTRFLLYTNENPNNFQLITGTEPDTIEASNFQLDRKTRFIIHGFLDKAEDSWPSDMCKKMFEVEKVNCICVDWRHGSRAMYTQAVQNIRVVGAETAFLIQALSTQLGYSLEDVHVIGHSLGAHTAAEAGRRLGGRVGRITGLDPAGPCFQDEPEEVRLDPSDAVFVDVIHTDSSPIVPSLGFGMSQKVGHLDFFPNGGKEMPGCKKNVLSTITDIDGIWEGIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPCPAEGCPKMGHYADQFKGKTSAVEQTFFLNTGESGNFT
2	P54317-D2	356-469	114		SWRYKISVTLSGKEKVNGYIRIALYGSNENSKQYEIFKGSLKPDASHTCAIDVDFNVGKIQKVKFLWNKRGINLSEPKLGASQITVQSGEDGTEYNFCSSDTVEENVLQSLYPC

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.85

(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	2pplA	0.93	1.26	0.629	0.953	model1_2pplA.pdb.gz
2	2pvsB	0.93	1.32	0.973	0.949	model1_2pvsB.pdb.gz
3	1ethA	0.90	1.61	0.625	0.927	model1_1ethA.pdb.gz
4	6e7kA	0.75	3.26	0.274	0.853	model1_6e7kA.pdb.gz
5	4qnnA	0.56	2.52	0.254	0.603	model1_4qnnA.pdb.gz
6	3e0xA	0.32	3.61	0.126	0.375	model1_3e0xA.pdb.gz
7	1xr2B2	0.31	6.78	0.051	0.488	model1_1xr2B2.pdb.gz
8	2b39A	0.30	7.29	0.038	0.486	model1_2b39A.pdb.gz
9	4i2wA1	0.28	7.85	0.041	0.484	model1_4i2wA1.pdb.gz
10	4m4dA	0.26	6.75	0.049	0.399	model1_4m4dA.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:0016787	0.99	hydrolase activity
GO:0016298	0.98	lipase activity
GO:0052689	0.78	carboxylic ester hydrolase activity
GO:0004806	0.74	triglyceride lipase activity
GO:1901363	0.64	heterocyclic compound binding
GO:0097159	0.64	organic cyclic compound binding
GO:0097367	0.62	carbohydrate derivative binding
GO:0005524	0.57	ATP 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:0008152	0.98	metabolic process
GO:0044699	0.93	single-organism process
GO:0071704	0.92	organic substance metabolic process
GO:0044710	0.92	single-organism metabolic process
GO:0044238	0.92	primary metabolic process
GO:0006629	0.87	lipid metabolic process
GO:0044237	0.84	cellular metabolic process
GO:0044763	0.76	single-organism cellular process
GO:0044255	0.67	cellular lipid metabolic process
GO:0034641	0.65	cellular nitrogen compound metabolic process
GO:0050896	0.61	response to stimulus
GO:0006643	0.60	membrane lipid metabolic process
GO:0016042	0.57	lipid catabolic process
GO:0044249	0.55	cellular biosynthetic process
GO:0008610	0.55	lipid biosynthetic process
GO:0046513	0.53	ceramide biosynthetic process
GO:0042221	0.53	response to chemical
GO:1901700	0.52	response to oxygen-containing compound
GO:0010033	0.52	response to organic substance

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:0044421	0.93	extracellular region part
GO:0005615	0.90	extracellular space
GO:0044464	0.85	cell part
GO:0044424	0.79	intracellular part
GO:0044444	0.73	cytoplasmic part
GO:0044446	0.71	intracellular organelle part
GO:0016020	0.68	membrane
GO:0044429	0.59	mitochondrial part
GO:0031090	0.56	organelle membrane
GO:0031966	0.53	mitochondrial membrane

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	0.671	1hplA	0.939	1.35	0.635	0.957	3.1.1.3	95,171,194,281
2	0.654	1lpaB	0.910	1.50	0.615	0.930	3.1.1.3	95,171,194,281
3	0.651	1gplA	0.908	0.99	0.715	0.921	3.1.1.3	94,170,193,280
4	0.643	1bu8A	0.925	1.47	0.785	0.951	3.1.1.3	94,170,193,280
5	0.633	1rp1A	0.922	1.34	0.637	0.940	3.1.1.3	95,171,194,281

	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	0.61	1lpbB	0.910	1.50	0.615	0.930	1.82	MUP	complex1.pdb.gz	95,96,170,171,172,197,199,234,282
2	0.02	3a70A	0.445	5.72	0.092	0.616	0.67	DEP	complex2.pdb.gz	95,96,137,171,172,235,282
3	0.01	2c5fA	0.408	5.13	0.083	0.527	0.51	NWA	complex3.pdb.gz	95,170,171,172
4	0.01	2wfzA	0.407	5.21	0.080	0.529	0.55	GD8	complex4.pdb.gz	94,95,170,171,172,280,285

	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.