D-I-TASSER Q6ZQW0

D-I-TASSER results for Q6ZQW0

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

Summary of the Protein

Uniprot ID: Q6ZQW0
Protein Name: Indoleamine 2,3-dioxygenase 2
Gene Name: IDO2

Input Sequence in FASTA format

>Q6ZQW0 (420 residues)
MLHFHYYDTSNKIMEPHRPNVKTAVPLSLESYHISEEYGFLLPDSLKELPDHYRPWMEIA
NKLPQLIDAHQLQAHVDKMPLLSCQFLKGHREQRLAHLVLSFLTMGYVWQEGEAQPAEVL
PRNLALPFVEVSRNLGLPPILVHSDLVLTNWTKKDPDGFLEIGNLETIISFPGGESLHGF
ILVTALVEKEAVPGIKALVQATNAILQPNQEALLQALQRLRLSIQDITKTLGQMHDYVDP
DIFYAGIRIFLSGWKDNPAMPAGLMYEGVSQEPLKYSGGSAAQSTVLHAFDEFLGIRHSK
ESGDFLYRMRDYMPPSHKAFIEDIHSAPSLRDYILSSGQDHLLTAYNQCVQALAELRSYH
ITMVTKYLITAAAKAKHGKPNHLPGPPQALKDRGTGGTAVMSFLKSVRDKTLESILHPRG

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	Q6ZQW0-D1	1-279	279		MLHFHYYDTSNKIMEPHRPNVKTAVPLSLESYHISEEYGFLLPDSLKELPDHYRPWMEIANKLPQLIDAHQLQAHVDKMPLLSCQFLKGHREQRLAHLVLSFLTMGYVWQEGEAQPAEVLPRNLALPFVEVSRNLGLPPILVHSDLVLTNWTKKDPDGFLEIGNLETIISFPGGESLHGFILVTALVEKEAVPGIKALVQATNAILQPNQEALLQALQRLRLSIQDITKTLGQMHDYVDPDIFYAGIRIFLSGWKDNPAMPAGLMYEGVSQEPLKYSGG
2	Q6ZQW0-D2	280-420	141		SAAQSTVLHAFDEFLGIRHSKESGDFLYRMRDYMPPSHKAFIEDIHSAPSLRDYILSSGQDHLLTAYNQCVQALAELRSYHITMVTKYLITAAAKAKHGKPNHLPGPPQALKDRGTGGTAVMSFLKSVRDKTLESILHPRG

Top 1 final models from D-I-TASSER

Click to view	Rank^a	Download	Estimated TM-score^b
	1	model1.pdb.gz	0.86

(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	2d0tB	0.86	1.23	0.445	0.883	model1_2d0tB.pdb.gz
2	2nwbA	0.70	2.69	0.146	0.769	model1_2nwbA.pdb.gz
3	2x68A	0.69	3.12	0.153	0.786	model1_2x68A.pdb.gz
4	4hkaA	0.46	3.01	0.158	0.514	model1_4hkaA.pdb.gz
5	3e08A	0.44	3.10	0.139	0.500	model1_3e08A.pdb.gz
6	2noxB	0.44	2.87	0.154	0.488	model1_2noxB.pdb.gz
7	4pw8A	0.39	2.77	0.130	0.429	model1_4pw8A.pdb.gz
8	1pz0A	0.27	5.68	0.054	0.386	model1_1pz0A.pdb.gz
9	2pocB	0.27	6.07	0.050	0.393	model1_2pocB.pdb.gz
10	3q5dA1	0.25	5.92	0.093	0.359	model1_3q5dA1.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:0003824	1.00	catalytic activity
GO:0016491	0.75	oxidoreductase activity
GO:0016702	0.66	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO:0033754	0.56	indoleamine 2,3-dioxygenase 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:1901564	1.00	organonitrogen compound metabolic process
GO:0006082	1.00	organic acid metabolic process
GO:1901605	0.95	alpha-amino acid metabolic process
GO:1901360	0.72	organic cyclic compound metabolic process
GO:0006725	0.72	cellular aromatic compound metabolic process
GO:0009072	0.69	aromatic amino acid family metabolic process
GO:0034641	0.67	cellular nitrogen compound metabolic process
GO:0046483	0.66	heterocycle metabolic process
GO:0006586	0.64	indolalkylamine metabolic process
GO:0006568	0.63	tryptophan metabolic process
GO:1901576	0.60	organic substance biosynthetic process
GO:1901575	0.60	organic substance catabolic process
GO:0044248	0.60	cellular catabolic process
GO:1901565	0.59	organonitrogen compound catabolic process
GO:1901361	0.59	organic cyclic compound catabolic process
GO:0044249	0.59	cellular biosynthetic process
GO:0019439	0.59	aromatic compound catabolic process
GO:0006569	0.58	tryptophan catabolic process
GO:0044711	0.54	single-organism biosynthetic process
GO:1901566	0.53	organonitrogen compound biosynthetic process
GO:0044238	0.52	primary metabolic process
GO:0019441	0.52	tryptophan catabolic process to kynurenine

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:0044444	0.92	cytoplasmic part
GO:0005829	0.69	cytosol
GO:0005737	0.68	cytoplasm

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	1thgA	0.352	6.69	0.052	0.562	3.1.1.3	NA
2	0.060	3e08A	0.440	3.10	0.139	0.500	1.13.11.11	NA
3	0.060	1j38A	0.349	7.03	0.045	0.567	3.4.15.1	NA
4	0.060	3ig5A	0.354	6.82	0.055	0.583	6.3.2.2	149
5	0.060	1ea0A	0.389	6.90	0.033	0.629	1.4.1.13	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:

Click to view	Rank	Cscore^LB	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov.	BS-score	Lig. Name	Download Complex	Predicted binding site residues
	1	0.08	2d0tA	0.863	1.14	0.446	0.881	0.77	UUU	complex1.pdb.gz	147,180,181,184,187,287,357,360,403,404,407
	2	0.01	1v97A	0.318	7.40	0.029	0.552	0.43	FES	complex2.pdb.gz	38,39,42,44,148

	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.