D-I-TASSER P39023

D-I-TASSER results for P39023

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

Summary of the Protein

Uniprot ID: P39023
Protein Name: 60S ribosomal protein L3
Gene Name: RPL3

Input Sequence in FASTA format

>P39023 (403 residues)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA

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	P39023-D1	1-81,205-403	280		MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKKEVVEAVTIVETVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
2	P39023-D2	82-204	123		PPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQ

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.972

(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	3j39B	0.98	1.15	0.747	1.000	model1_3j39B.pdb.gz
2	3jctB	0.94	0.97	0.671	0.958	model1_3jctB.pdb.gz
3	3zf7f	0.94	1.64	0.589	0.985	model1_3zf7f.pdb.gz
4	1vx7E	0.93	0.75	0.650	0.943	model1_1vx7E.pdb.gz
5	4a17B	0.93	1.49	0.622	0.958	model1_4a17B.pdb.gz
6	5xy3B	0.92	1.27	0.579	0.943	model1_5xy3B.pdb.gz
7	5an9A	0.90	2.31	0.562	0.955	model1_5an9A.pdb.gz
8	3iz5C	0.89	2.27	0.617	0.953	model1_3iz5C.pdb.gz
9	3j21C	0.79	2.38	0.382	0.851	model1_3j21C.pdb.gz
10	3cxcB	0.77	1.96	0.352	0.819	model1_3cxcB.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:0003735	1.00	structural constituent of ribosome
GO:1901363	0.63	heterocyclic compound binding
GO:0097159	0.63	organic cyclic compound 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:0009987	1.00	cellular process
GO:0006412	0.99	translation
GO:0022618	0.98	ribonucleoprotein complex assembly
GO:0000027	0.97	ribosomal large subunit assembly

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:0044446	0.99	intracellular organelle part
GO:0044444	0.97	cytoplasmic part
GO:0030529	0.96	intracellular ribonucleoprotein complex
GO:0022625	0.94	cytosolic large ribosomal subunit

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	2iukB	0.319	7.03	0.030	0.541	1.13.11.12	NA
2	0.060	3cirM	0.261	7.05	0.044	0.439	1.3.99.1	276
3	0.060	2vdcA	0.326	6.95	0.040	0.541	1.4.1.13	NA
4	0.060	2x6fA	0.306	7.16	0.050	0.516	2.7.1.137 2.7.1.153 2.7.1.154	NA
5	0.060	2x58A	0.308	6.63	0.058	0.491	5.3.3.8 4.2.1.17 1.1.1.35	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	1w7i0	0.254	7.41	0.041	0.449	0.20	III	complex1.pdb.gz	78,80,343,344
2	0.01	2hgq4	0.095	3.71	0.143	0.114	0.25	III	complex2.pdb.gz	48,82,84,109,110,347
3	0.01	1ry2A	0.328	6.83	0.038	0.536	0.16	AMP	complex3.pdb.gz	82,83,326
4	0.01	1jnqA	0.321	6.60	0.034	0.519	0.14	UUU	complex4.pdb.gz	45,46,81,179,219
5	0.01	2bteA	0.307	7.47	0.040	0.546	0.16	LEU	complex5.pdb.gz	49,50,51,52
6	0.01	1obcA	0.331	6.86	0.037	0.556	0.22	UUU	complex6.pdb.gz	47,48,84,85,87,182
7	0.01	2bteA	0.307	7.47	0.040	0.546	0.14	UUU	complex7.pdb.gz	48,49,83,84
8	0.01	3ottB	0.350	6.90	0.052	0.573	0.15	TBR	complex8.pdb.gz	52,53,76,221
9	0.01	2vdcA	0.326	6.95	0.040	0.541	0.15	FMN	complex9.pdb.gz	81,173,339
10	0.01	1r9dA	0.270	7.24	0.034	0.467	0.25	GOL	complex10.pdb.gz	77,281,283

	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.