D-I-TASSER P08571

D-I-TASSER results for P08571

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Summary of the Protein

Uniprot ID: P08571
Protein Name: Monocyte differentiation antigen CD14
Gene Name: CD14

Input Sequence in FASTA format

>P08571 (375 residues)
MERASCLLLLLLPLVHVSATTPEPCELDDEDFRCVCNFSEPQPDWSEAFQCVSAVEVEIH
AGGLNLEPFLKRVDADADPRQYADTVKALRVRRLTVGAAQVPAQLLVGALRVLAYSRLKE
LTLEDLKITGTMPPLPLEATGLALSSLRLRNVSWATGRSWLAELQQWLKPGLKVLSIAQA
HSPAFSCEQVRAFPALTSLDLSDNPGLGERGLMAALCPHKFPAIQNLALRNTGMETPTGV
CAALAAAGVQPHSLDLSHNSLRATVNPSAPRCMWSSALNSLNLSFAGLEQVPKGLPAKLR
VLDLSCNRLNRAPQPDELPEVDNLTLDGNPFLVPGTALPHEGSMNSGVVPACARSTLSVG
VSGTLVLLQGARGFA

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	P08571-D1	1-375	375		MERASCLLLLLLPLVHVSATTPEPCELDDEDFRCVCNFSEPQPDWSEAFQCVSAVEVEIHAGGLNLEPFLKRVDADADPRQYADTVKALRVRRLTVGAAQVPAQLLVGALRVLAYSRLKELTLEDLKITGTMPPLPLEATGLALSSLRLRNVSWATGRSWLAELQQWLKPGLKVLSIAQAHSPAFSCEQVRAFPALTSLDLSDNPGLGERGLMAALCPHKFPAIQNLALRNTGMETPTGVCAALAAAGVQPHSLDLSHNSLRATVNPSAPRCMWSSALNSLNLSFAGLEQVPKGLPAKLRVLDLSCNRLNRAPQPDELPEVDNLTLDGNPFLVPGTALPHEGSMNSGVVPACARSTLSVGVSGTLVLLQGARGFA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.8264

(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	3a79A	0.80	3.68	0.179	0.933	model1_3a79A.pdb.gz
2	2id5B1	0.77	3.77	0.149	0.912	model1_2id5B1.pdb.gz
3	2a0zA	0.76	3.78	0.156	0.915	model1_2a0zA.pdb.gz
4	2z7xB	0.76	4.13	0.143	0.941	model1_2z7xB.pdb.gz
5	3rg1A	0.76	3.70	0.155	0.909	model1_3rg1A.pdb.gz
6	5gmfA	0.76	3.87	0.172	0.912	model1_5gmfA.pdb.gz
7	4lxrA	0.76	3.66	0.126	0.901	model1_4lxrA.pdb.gz
8	6zjzA	0.76	3.89	0.133	0.923	model1_6zjzA.pdb.gz
9	3wpbA	0.75	3.99	0.167	0.923	model1_3wpbA.pdb.gz
10	3v44A	0.75	3.82	0.156	0.909	model1_3v44A.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:0004872	0.74	receptor 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:0065007	0.90	biological regulation
GO:0050789	0.90	regulation of biological process
GO:0048518	0.85	positive regulation of biological process
GO:0048583	0.84	regulation of response to stimulus
GO:0050794	0.83	regulation of cellular process
GO:0048584	0.82	positive regulation of response to stimulus
GO:0009987	0.81	cellular process
GO:0002376	0.81	immune system process
GO:0002684	0.80	positive regulation of immune system process
GO:0002253	0.79	activation of immune response
GO:0007165	0.78	signal transduction
GO:0002224	0.75	toll-like receptor signaling pathway
GO:0050896	0.74	response to stimulus
GO:0010033	0.72	response to organic substance
GO:0043207	0.71	response to external biotic stimulus
GO:0002237	0.70	response to molecule of bacterial origin
GO:0032493	0.68	response to bacterial lipoprotein
GO:0071727	0.64	cellular response to triacyl bacterial lipopeptide
GO:0071726	0.59	cellular response to diacyl bacterial lipopeptide
GO:0051239	0.57	regulation of multicellular organismal process
GO:0051240	0.56	positive regulation of multicellular organismal process
GO:0001817	0.54	regulation of cytokine production
GO:0001819	0.53	positive regulation of cytokine production

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:0044425	0.88	membrane part
GO:0044424	0.80	intracellular part
GO:0016020	0.78	membrane
GO:0044459	0.74	plasma membrane part
GO:0031224	0.74	intrinsic component of membrane
GO:0044444	0.73	cytoplasmic part
GO:0031226	0.73	intrinsic component of plasma membrane
GO:0043227	0.71	membrane-bounded organelle
GO:0043231	0.68	intracellular membrane-bounded organelle
GO:0098589	0.63	membrane region
GO:0045121	0.62	membrane raft
GO:0005794	0.62	Golgi apparatus
GO:0032991	0.54	macromolecular complex
GO:0043234	0.53	protein complex
GO:0098796	0.51	membrane protein complex
GO:0043235	0.51	receptor complex

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	2nq5A	0.409	5.87	0.047	0.616	2.1.1.14	154
2	0.060	1oocB	0.444	6.03	0.085	0.677	4.2.2.2	128,151
3	0.060	1uyvA	0.413	6.68	0.053	0.685	6.3.4.14 6.4.1.2	NA
4	0.060	1vblA	0.418	6.13	0.036	0.648	4.2.2.2	NA
5	0.060	3figB	0.422	7.00	0.070	0.728	2.3.3.13	153

	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	0.07	3a79B	0.746	4.15	0.181	0.925	0.67	UUU	complex1.pdb.gz	129,130,153,181
2	0.06	3rg1A	0.760	3.70	0.155	0.909	0.43	UUU	complex2.pdb.gz	130,155,156,180,182,183
3	0.05	2z7xA	0.802	3.48	0.169	0.928	1.10	PCJ	complex3.pdb.gz	110,121,147,152,156,157,158,159,167,180,181,182,183,184,185,186,211
4	0.04	2z82A	0.789	3.78	0.182	0.931	0.68	PDJ	complex4.pdb.gz	130,132,147,149,180,193,201,206,207,208,212,214,217
5	0.04	3a7bA	0.780	3.78	0.171	0.928	0.81	LTC	complex5.pdb.gz	128,131,135,149,152,153,154,164,181
6	0.04	3a79A	0.796	3.68	0.179	0.933	0.50	III	complex6.pdb.gz	130,155,156,183
7	0.04	2z81A	0.788	3.78	0.182	0.931	0.47	PCJ	complex7.pdb.gz	58,60,89,94,96,123,133
8	0.03	1z7x2	0.722	4.67	0.139	0.944	0.43	III	complex8.pdb.gz	93,97,122,124,176,198,226,230

	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.