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# D-I-TASSER results for P07998

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

Summary of the Protein

Uniprot ID: P07998
Protein Name: Ribonuclease pancreatic
Gene Name: RNASE1

Input Sequence in FASTA format

>P07998 (156 residues) MALEKSLVRLLLLVLILLVLGWVQPSLGKESRAKKFQRQHMDSDSSPSSSSTYCNQMMRR RNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRY PNCAYRTSPKERHIIVACEGSPYVPVHFDASVEDST

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 | P07998-D1 | 1-156 | 156 |  | MALEKSLVRLLLLVLILLVLGWVQPSLGKESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQNVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEGSPYVPVHFDASVEDST

Top 1 final models from D-I-TASSER

Click to view | Ranka | Download | Estimated TM-scoreb
| 1 | model1.pdb.gz | 0.7147
(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)
Click to view | Rank | PDB Hit | TM-score | RMSDa | IDENa | Cov. | Download Alignment
--- | --- | --- | --- | --- | --- | --- | ---
| 1 | 3mwqA | 0.84 | 2.20 | 0.592 | 0.917 | model1_3mwqA.pdb.gz
| 2 | 1rraA | 0.77 | 0.98 | 0.653 | 0.795 | model1_1rraA.pdb.gz
| 3 | 2rnfA | 0.72 | 1.32 | 0.433 | 0.763 | model1_2rnfA.pdb.gz
| 4 | 4x09A | 0.69 | 1.72 | 0.361 | 0.750 | model1_4x09A.pdb.gz
| 5 | 2zpoA | 0.69 | 1.89 | 0.414 | 0.744 | model1_2zpoA.pdb.gz
| 6 | 1qmtA | 0.68 | 1.87 | 0.333 | 0.750 | model1_1qmtA.pdb.gz
| 7 | 1k2aA | 0.68 | 1.98 | 0.339 | 0.750 | model1_1k2aA.pdb.gz
| 8 | 1k59A | 0.68 | 1.84 | 0.353 | 0.744 | model1_1k59A.pdb.gz
| 9 | 2j4tA | 0.68 | 1.82 | 0.379 | 0.744 | model1_2j4tA.pdb.gz
| 10 | 2vq9A | 0.68 | 1.83 | 0.328 | 0.744 | model1_2vq9A.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) | RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d) | IDENa 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 | CscoreGO | Name
GO:0004540 | 1.00 | ribonuclease activity
GO:0004519 | 0.89 | endonuclease activity
Download full result of the above consensus prediction.

| Click the graph to show a high resolution version.
(a) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[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 | CscoreGO | Name
GO:0009987 | 0.96 | cellular process
GO:0071704 | 0.94 | organic substance metabolic process
GO:1901360 | 0.93 | organic cyclic compound metabolic process
GO:0044699 | 0.93 | single-organism process
GO:0044238 | 0.93 | primary metabolic process
GO:0034641 | 0.93 | cellular nitrogen compound metabolic process
GO:0016070 | 0.92 | RNA metabolic process
GO:0065007 | 0.88 | biological regulation
GO:0050896 | 0.85 | response to stimulus
GO:0050794 | 0.83 | regulation of cellular process
GO:0006950 | 0.83 | response to stress
GO:0048522 | 0.81 | positive regulation of cellular process
GO:0044767 | 0.80 | single-organism developmental process
GO:0044763 | 0.80 | single-organism cellular process
GO:0032879 | 0.78 | regulation of localization
GO:0090501 | 0.77 | RNA phosphodiester bond hydrolysis
GO:0090502 | 0.76 | RNA phosphodiester bond hydrolysis, endonucleolytic
GO:0048646 | 0.76 | anatomical structure formation involved in morphogenesis
GO:0044710 | 0.74 | single-organism metabolic process
GO:0050790 | 0.72 | regulation of catalytic activity
GO:0016043 | 0.72 | cellular component organization
GO:1901576 | 0.71 | organic substance biosynthetic process
GO:0048523 | 0.71 | negative regulation of cellular process
GO:0044271 | 0.71 | cellular nitrogen compound biosynthetic process
GO:0008284 | 0.71 | positive regulation of cell proliferation
GO:0051223 | 0.70 | regulation of protein transport
GO:0051050 | 0.70 | positive regulation of transport
GO:0044711 | 0.70 | single-organism biosynthetic process
GO:0006629 | 0.70 | lipid metabolic process
GO:0006351 | 0.70 | transcription, DNA-templated
GO:1903532 | 0.69 | positive regulation of secretion by cell
GO:0098781 | 0.69 | ncRNA transcription
GO:0051258 | 0.69 | protein polymerization
GO:0050708 | 0.69 | regulation of protein secretion
GO:0050679 | 0.69 | positive regulation of epithelial cell proliferation
GO:0048660 | 0.69 | regulation of smooth muscle cell proliferation
GO:0046463 | 0.69 | acylglycerol biosynthetic process
GO:0046339 | 0.69 | diacylglycerol metabolic process
GO:0036293 | 0.69 | response to decreased oxygen levels
GO:0032430 | 0.69 | positive regulation of phospholipase A2 activity
GO:0010863 | 0.69 | positive regulation of phospholipase C activity
GO:0008285 | 0.69 | negative regulation of cell proliferation
GO:0008154 | 0.69 | actin polymerization or depolymerization
GO:0001936 | 0.69 | regulation of endothelial cell proliferation
GO:0051222 | 0.65 | positive regulation of protein transport
GO:0001525 | 0.61 | angiogenesis
GO:0009605 | 0.54 | response to external stimulus
GO:0006952 | 0.54 | defense response
GO:0051704 | 0.53 | multi-organism process
GO:0042742 | 0.52 | defense response to bacterium
GO:0050714 | 0.50 | positive regulation of protein secretion
GO:0048856 | 0.50 | anatomical structure development
GO:0048662 | 0.50 | negative regulation of smooth muscle cell proliferation
GO:0032431 | 0.50 | activation of phospholipase A2 activity
GO:0030041 | 0.50 | actin filament polymerization
GO:0009303 | 0.50 | rRNA transcription
GO:0007202 | 0.50 | activation of phospholipase C activity
GO:0006651 | 0.50 | diacylglycerol biosynthetic process
GO:0001938 | 0.50 | positive regulation of endothelial cell proliferation
GO:0001666 | 0.50 | response to hypoxia

Download full result of the above consensus prediction.

| Click the graph to show a high resolution version.
(a) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[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 | CscoreGO | Name
GO:0043227 | 0.93 | membrane-bounded organelle
GO:0044421 | 0.86 | extracellular region part
GO:0044464 | 0.81 | cell part
GO:0044424 | 0.78 | intracellular part
GO:0043229 | 0.63 | intracellular organelle
GO:0043231 | 0.62 | intracellular membrane-bounded organelle
GO:0044446 | 0.57 | intracellular organelle part
GO:0005634 | 0.55 | nucleus
GO:0043234 | 0.53 | protein complex
GO:0032311 | 0.52 | angiogenin-PRI complex
GO:0005615 | 0.51 | extracellular space

Download full result of the above consensus prediction.

| Click the graph to show a high resolution version.
(a) | CscoreGO is the confidence score of predicted GO terms. CscoreGO 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 CscoreGO:
[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
Click to view | Rank | CscoreEC | PDB Hit | TM-score | RMSDa | IDENa | Cov. | EC Number | Predicted Active Site Residues
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
| 1 | 0.179 | 1rnfA | 0.724 | 1.31 | 0.433 | 0.763 | 3.1.27.- | NA
| 2 | 0.178 | 2rnfA | 0.724 | 1.32 | 0.433 | 0.763 | 4.2.1.81 | NA
| 3 | 0.176 | 1rraA | 0.767 | 0.98 | 0.653 | 0.795 | 3.1.27.5 | NA
| 4 | 0.173 | 2e0jA | 0.781 | 1.24 | 0.984 | 0.821 | 3.1.27.5 | NA
| 5 | 0.148 | 1agiA | 0.696 | 2.06 | 0.331 | 0.776 | 3.1.27.- | NA
| Click on the radio buttons to visualize predicted active site residues.
(a) | CscoreEC is the confidence score for the Enzyme Commission (EC) number prediction. CscoreEC 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) | RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d) | IDENa 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:
Click to view | Rank | CscoreLB | PDB Hit | TM-score | RMSDa | IDENa | Cov. | BS-score | Lig. Name | Download Complex | Predicted binding site residues
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
| 1 | 0.57 | 3srnA | 0.711 | 0.72 | 0.673 | 0.724 | 1.68 | III | complex1.pdb.gz | 32,33,36,40,73,75,83,86,93,94,99,100,101,102,109,132,133,134,135,136,137,138,139,140
| 2 | 0.37 | 1dfj0 | 0.779 | 0.66 | 0.702 | 0.795 | 1.78 | III | complex2.pdb.gz | 35,39,52,59,60,63,66,67,69,70,71,94,95,99,114,116,117,119,137,139,147
| 3 | 0.37 | 9rsa0 | 0.785 | 0.54 | 0.702 | 0.795 | 1.74 | III | complex3.pdb.gz | 70,89,90,91,92,93,94,111,113,114,116,126,128,132,135,149,152
| 4 | 0.36 | 1jn4A | 0.780 | 0.66 | 0.702 | 0.795 | 1.49 | 139 | complex4.pdb.gz | 39,40,71,72,73,93,95,97,99,137,139,146,147,148
| Click on the radio buttons to visualize predicted binding site and residues.
(a) | CscoreLB is the confidence score of predicted binding site. CscoreLB 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) | RMSDa the RMSD between residues that are structurally aligned by TM-align.
(e) | IDENa 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.