D-I-TASSER P09001

D-I-TASSER results for P09001

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

Summary of the Protein

Uniprot ID: P09001
Protein Name: 39S ribosomal protein L3, mitochondrial
Gene Name: MRPL3

Input Sequence in FASTA format

>P09001 (348 residues)
MPGWRLLTQVGAQVLGRLGDGLGAALGPGNRTHIWLFVRGLHGKSGTWWDEHLSEENVPF
IKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKLGMMPLWTKDGQKHVVT
LLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFN
ITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRP
GAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVK
DSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA

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	P09001-D1	1-348	348		MPGWRLLTQVGAQVLGRLGDGLGAALGPGNRTHIWLFVRGLHGKSGTWWDEHLSEENVPFIKQLVSDEDKAQLASKLCPLKDEPWPIHPWEPGSFRVGLIALKLGMMPLWTKDGQKHVVTLLQVQDCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFNITDNAAIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRPGAVATGDIGRVWPGTKMPGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGHKNCLVKVKDSKLPAYKDLGKNLPFPTYFPDGDEEELPEDLYDENVCQPGAPSITFA

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.805

(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	4v19E	0.88	0.55	0.893	0.882	model1_4v19E.pdb.gz
2	7oodb	0.60	2.01	0.223	0.638	model1_7oodb.pdb.gz
3	1vw3C	0.59	1.70	0.338	0.618	model1_1vw3C.pdb.gz
4	5o60D	0.58	1.40	0.310	0.603	model1_5o60D.pdb.gz
5	8cvmd	0.58	1.80	0.300	0.612	model1_8cvmd.pdb.gz
6	5mmmD	0.58	2.11	0.275	0.615	model1_5mmmD.pdb.gz
7	5li0E	0.57	1.67	0.306	0.601	model1_5li0E.pdb.gz
8	6yhsB	0.57	1.57	0.298	0.598	model1_6yhsB.pdb.gz
9	5v7qD	0.57	1.64	0.298	0.598	model1_5v7qD.pdb.gz
10	3i1rD	0.57	1.66	0.304	0.595	model1_3i1rD.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	0.80	structural constituent of ribosome
GO:1901363	0.74	heterocyclic compound binding
GO:0097159	0.74	organic cyclic compound binding
GO:0003676	0.58	nucleic acid binding
GO:0003723	0.57	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:0009987	0.97	cellular process
GO:0008152	0.97	metabolic process
GO:0071704	0.96	organic substance metabolic process
GO:0044237	0.96	cellular metabolic process
GO:0044260	0.95	cellular macromolecule metabolic process
GO:0034645	0.94	cellular macromolecule biosynthetic process
GO:0044238	0.89	primary metabolic process
GO:0034641	0.88	cellular nitrogen compound metabolic process
GO:1901564	0.85	organonitrogen compound metabolic process
GO:0044271	0.85	cellular nitrogen compound biosynthetic process
GO:0006412	0.84	translation
GO:0071840	0.53	cellular component organization or biogenesis
GO:0016043	0.52	cellular component organization

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:0044444	1.00	cytoplasmic part
GO:0044446	0.95	intracellular organelle part
GO:0030529	0.91	intracellular ribonucleoprotein complex
GO:0015934	0.90	large ribosomal subunit
GO:0044429	0.69	mitochondrial part
GO:0005762	0.64	mitochondrial large ribosomal subunit
GO:0043226	0.50	organelle

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	2jfdA	0.249	7.03	0.037	0.431	2.3.1.85	NA
2	0.060	1mo7A	0.192	5.89	0.000	0.302	3.6.3.9	301
3	0.060	1fo4A	0.325	6.76	0.037	0.552	1.17.1.4	NA
4	0.060	1cf3A	0.311	6.84	0.040	0.534	1.1.3.4	NA
5	0.060	1rw9A	0.308	6.57	0.033	0.517	4.2.2.5	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	1vs88	0.190	4.29	0.068	0.244	0.25	III	complex1.pdb.gz	116,117,118
2	0.01	3kdpA	0.334	6.88	0.034	0.589	0.17	MF4	complex2.pdb.gz	104,105,106
3	0.01	1rm6A	0.351	6.59	0.031	0.581	0.10	PCD	complex3.pdb.gz	95,300,301,302
4	0.01	3opyB	0.336	6.52	0.026	0.560	0.25	ATP	complex4.pdb.gz	104,107,119
5	0.01	3cmvH	0.277	6.87	0.038	0.486	0.21	ANP	complex5.pdb.gz	102,103,104,105,287
6	0.01	3cmvD	0.291	6.92	0.031	0.506	0.14	ANP	complex6.pdb.gz	102,103,104,105
7	0.01	2uvcG	0.333	6.48	0.027	0.557	0.15	FMN	complex7.pdb.gz	99,148,177
8	0.01	3cmvE	0.255	7.21	0.024	0.463	0.31	ANP	complex8.pdb.gz	99,101,270

	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.