D-I-TASSER results for Q8NDZ0

Summary of the Protein

Uniprot ID: Q8NDZ0


Protein Name: BEN domain-containing protein 2


Gene Name: BEND2

Input Sequence in FASTA format

>Q8NDZ0 (799 residues)
MSERTQEQDFVIITVDDSDDNNDCSIEMVEVSETADNSTNDIADDSTYVTADNPTDDTAT
QPNFPGGNDGHHRPLQMSYGSGSVTQAGVQWHDHSSLQPQPLGLKQFFHLSLPSSWDDRR
TPPCPVAHGDQIVSQINHPVHLRRYSYNSEEVDFPKRGRFYTPEVQSSISPPAERQETHA
WASPAVTSLESAACHELQEADLSESLSYPRIVSSSSLQQYVAQGGSFPCFGMPWNFISGG
AESTNAVISFANATTAVPMAVLSRRESSLANNPGVVNYSALPENENVGPGRALSSFCFHP
NLEMPERPANSSKNSTETANYPTLMGNYNGQNTASLSVFIPPYFAEKIILTEMPGTTETN
VENNSQTVYYPALSGNTSAPYPASSYLPITSNFESGPQMSYGTMSYSTEMKNNCDQDDAS
ASACLTPDFALLPLNILVKVDTNTENSVNTMNRSTLLDSDSGQDSSSSSVCIPPKYGYLG
DPKRNVRVLKIHLLAVQNMAKPKQAACYLVRILFSKEILISSSVDIHLKDSQSLDPNKMA
ALREYLATTFPTCDLHEHGKDWQDCISGINSMIYCLCSEGKSTPKTVRKNKKRTNRVASA
SADRNDQRGRDGGEGCSWMFQPMNNSKMREKRNLQPNSNAIPEGMREPSTDNPEEPGEAW
SYFGRPWRNIRMPCSVLTLAKTKSCASLSARYLIQKLFTKDVLVQSNVYGNLKHGLCALD
PNKISALREFLQENYPICDLSENGRDWKSCVTSINSGIRSLRHDVRRAEARSQSLPAVTP
PELEQESKPGDPDATDPST

Predicted Contact and Distance Map Used in D-I-TASSER simulation

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	Sequence
1	Q8NDZ0-D1	1-799	799	MSERTQEQDFVIITVDDSDDNNDCSIEMVEVSETADNSTNDIADDSTYVTADNPTDDTATQPNFPGGNDGHHRPLQMSYGSGSVTQAGVQWHDHSSLQPQPLGLKQFFHLSLPSSWDDRRTPPCPVAHGDQIVSQINHPVHLRRYSYNSEEVDFPKRGRFYTPEVQSSISPPAERQETHAWASPAVTSLESAACHELQEADLSESLSYPRIVSSSSLQQYVAQGGSFPCFGMPWNFISGGAESTNAVISFANATTAVPMAVLSRRESSLANNPGVVNYSALPENENVGPGRALSSFCFHPNLEMPERPANSSKNSTETANYPTLMGNYNGQNTASLSVFIPPYFAEKIILTEMPGTTETNVENNSQTVYYPALSGNTSAPYPASSYLPITSNFESGPQMSYGTMSYSTEMKNNCDQDDASASACLTPDFALLPLNILVKVDTNTENSVNTMNRSTLLDSDSGQDSSSSSVCIPPKYGYLGDPKRNVRVLKIHLLAVQNMAKPKQAACYLVRILFSKEILISSSVDIHLKDSQSLDPNKMAALREYLATTFPTCDLHEHGKDWQDCISGINSMIYCLCSEGKSTPKTVRKNKKRTNRVASASADRNDQRGRDGGEGCSWMFQPMNNSKMREKRNLQPNSNAIPEGMREPSTDNPEEPGEAWSYFGRPWRNIRMPCSVLTLAKTKSCASLSARYLIQKLFTKDVLVQSNVYGNLKHGLCALDPNKISALREFLQENYPICDLSENGRDWKSCVTSINSGIRSLRHDVRRAEARSQSLPAVTPPELEQESKPGDPDATDPST

Top 1 final models from D-I-TASSER

Rank^a	Estimated TM-score^b
1	0.4442


(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.
1	6zwmE	0.87	2.72	0.081	0.920
2	3gjxA	0.48	7.33	0.050	0.690
3	6yejA	0.48	6.43	0.063	0.646
4	7dxjA	0.48	7.52	0.049	0.698
5	6q82A	0.47	7.91	0.061	0.715
6	6xjpC	0.47	6.96	0.029	0.663
7	2x19B	0.46	6.78	0.054	0.639
8	1qgkA	0.45	7.44	0.051	0.655
9	5gm6G	0.45	6.71	0.039	0.611
10	5dlqB	0.44	6.93	0.053	0.621



(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:1901363	0.65	heterocyclic compound binding
GO:0097159	0.65	organic cyclic compound binding






(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:

Biological Process (BP)


GO term	Cscore^GO	Name
GO:0048741	1.00	skeletal muscle fiber development






(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:

Cellular Component (CC)


GO term	Cscore^GO	Name
GO:0044446	1.00	intracellular organelle part
GO:0005737	1.00	cytoplasm
GO:0043226	0.97	organelle
GO:0043229	0.96	intracellular organelle
GO:0043227	0.96	membrane-bounded organelle
GO:0043231	0.95	intracellular membrane-bounded organelle
GO:0005634	0.92	nucleus
GO:0044428	0.91	nuclear part
GO:0016020	0.76	membrane
GO:0044444	0.68	cytoplasmic part
GO:0031965	0.64	nuclear membrane
GO:0032991	0.52	macromolecular complex






(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:

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	3ebgA	0.321	7.94	0.037	0.484	3.4.11.-	NA
2	0.060	3hkzJ	0.278	8.37	0.031	0.432	2.7.7.6	NA
3	0.060	2qf7B	0.219	8.40	0.029	0.345	6.4.1.1	651
4	0.060	2ebsB	0.273	8.23	0.050	0.425	3.2.1.150	NA
5	0.060	3b9jJ	0.155	7.00	0.047	0.219	1.17.1.4 1.17.3.2	NA



(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	Predicted binding site residues
1	0.01	1qgrA	0.441	7.38	0.058	0.641	0.11	III	85,89,135,230
2	0.01	3k5qA	0.327	4.77	0.064	0.392	0.12	QNA	58,86,88,131,133,134,137,179,362,403,406
3	0.01	2ot8A	0.347	7.39	0.042	0.502	0.13	III	85,88,129
4	0.01	3k5yA	0.327	4.60	0.062	0.388	0.12	QNA	54,85,88,131
5	0.01	2ie40	0.354	5.83	0.035	0.458	0.21	III	86,125,172
6	0.01	3c2gB	0.333	6.28	0.045	0.446	0.16	III	89,133,135,138
7	0.01	3c2gA	0.324	6.67	0.044	0.446	0.15	III	146,147,153,230
8	0.01	2ot8B	0.378	6.98	0.054	0.529	0.14	III	54,58,88,130,135,177
9	0.01	2ot8A	0.347	7.39	0.042	0.502	0.11	III	89,225,226,229,236



(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.

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.