Table 4.
Results of the template search; 14 structures were found using the programs 3D Jury, Superfamily –“Superfam“, Phyre, Libellula “Lib“, HHPred; the programs Wurst and Loop yielded only false positive template structures. The six templates found with 3D-Jury are printed in bold.
| No | Protein Name | PDB entry |
Method | Template Score for Laminin β1; γ1 |
SCOP Fold name |
SCOP Fold classification code |
CATH Fold name |
CATH Fold classification code |
Protein Function Gene Ontology Annotation |
Reference |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | factor V | 1CZT |
3DJury HHPred* |
52; 58 95; 87 |
Galactose-binding domain-like |
49784 |
Galactose-binding domain-like |
2.60.120.260 | Blood Clotting | (47) |
| 2 | factor VIII | 1D7P |
3D Jury HHPred |
42; 57 88; 82 |
Galactose-binding domain-like |
49784 |
Galactose-binding domain-like |
2.60.120.260 | Blood Clotting | (48) |
| 3 | Sialidase | 1EUT | Libellula, Phyre* |
25%; 80% | Galactose-binding domain-like |
49784 | Galactose-binding domain-like |
2.60.120.260 | Hydrolase | (49) |
| 4 | Galactose oxidase | 1GOF | 3DJury | 49; 50 |
Galactose-binding domain-like |
49784 |
Galactose-binding domain-like |
2.60.120.260 | Oxidoreductase(Oxygen(A)) | (50) |
| 5 | APC10/DOC1 subunit of the anaphase- promoting complex |
1GQP | Phyre HHPred* |
-; 30% -; 74 |
Galactose-binding domain-like |
49784 | Galactose-binding domain-like |
2.60.120.260 | Cell Cycle | (51) |
| 6 | Carbohydrate binding module from laminarinase 16A |
1GUI | Libellula | Galactose-binding domain-like |
49784 | Galactose-binding domain-like |
2.60.120.260 | Carbohydrate Binding Module |
(52) | |
| 7 | APC10/DOC1 subunit of the anaphase- promoting complex |
1JHJ | Phyre HHPred* |
-; 25% -; 48 |
Galactose-binding domain-like |
49784 | Galactose-binding domain-like |
2.60.120.260 | Cell Cycle | (53) |
| 8 | Fucose binding lectin |
1K12 | HHPred* | 94; 95 | Galactose-binding domain-like |
49784 | Galactose-binding domain-like |
2.60.120.260 | Sugar Binding Protein | (54) |
| 9 | Galactose oxidase | 1K3I | Phyre HHPred |
30%; 80% 96; 95 |
Galactose-binding domain-like |
49784 | Galactose-binding domain-like |
2.60.120.260 | Oxidoreductase | (55) |
| 10 |
B1 domain of neuropilin-1 |
1KEX |
3D-Jury HHPred |
37; 53 96; 93 |
Galactose-binding domain-like |
49784 |
Galactose-binding domain-like |
2.60.120.260 | Protein Binding | (56) |
| 11 |
Coagulation factor V |
1SDD |
3DJury HHPred Phyre |
49; 39 67; 41 94%; 94% |
Galactose-binding domain-like |
49784 |
Galactose-binding domain-like |
2.60.120.260 | Blood Clotting | (57) |
| 12 | Placental protein 25, pp25 |
1TVG | HHPred Phyre |
54; 53 98%; 97% |
Galactose-binding domain-like |
49784 | Galactose-binding domain-like |
2.60.120.260 | Cell Cycle | (58) |
| 13 | xrcc1 | 1XNA | Libellula | Galactose-binding domain-like |
49784 | Galactose-binding domain-like |
2.60.120.260 | DNA Binding Protein | (59) | |
| 14 |
Placental protein 25, pp25 |
1XPW | 3DJury | 47; 50 |
Galactose-binding domain-like |
49784 |
Galactose-binding domain-like |
2.60.120.260 |
Structural Genomics, Unknown Function |
(58) |
| 15 | chitobiase (N- acetyl-beta- glucoseaminidase) |
1QBA | Phyre | 45%; - | Immunoglobulin- like beta-sandwich |
[48725] | Chitobiase, domain 2 |
3.30.379.10 | Glycosyl Hydrolase | (60) |
| 16 | Hypothetical protein TM1631 |
1VPQ | Wurst | 9.4; - | TIM beta/alpha- barrel |
[51350] | Hypothetical protein tm1631. |
3.20.20.410 | Structural Genomics, Unknown Function |
(61) |
| 17 | Class I MHC | 1HSB | Wurst | 9.3; - | Immunoglobulin- like beta-sandwich |
[48725] | Immunoglobulins | 2.60.40.10 | Histocompatibility Antigen | (62) |
| 18 | Cu,Zn superoxide dismutase |
1TO4 | Wurst | 9.1; - | Immunoglobulin- like beta-sandwich |
[48725] | Immunoglobulin- like |
2.60.40.200 | Oxidoreductase | (63) |
| 19 | Putative regulator protein YcfX |
1AP1 | Wurst | 9.1; - | Ribonuclease H- like motif |
[53066] | Not yet assigned |
Transferase | (64) | |
| 20 | Alginate-binding periplasmic protein AlgQ1 |
1Y3N | Wurst | 9.1; - | Periplasmic binding protein-like II |
[53849] | Periplasmic binding protein- like II |
3.40.190.10 | Sugar Binding Protein | (65) |
| 21 | Myo-inositol 1- phosphate synthase |
1VKO | Wurst | -; 11.0 | AD(P)-binding Rossmann-fold domains |
[51734] | Not yet assigned |
Isomerase | (66) | |
| 22 | c-KIT receptor | 1T46 | Wurst | -; 10.0 | Protein kinase-like (PK-like) |
[56111] | Phosphorylase Kinase; domain 1 |
3.30.200.20 | Transferase Activator | (67) |
| 23 | Interleukin-8 | 1ILQ | Wurst | -; 10.0 | IL8-like | [54116] | OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
2.40.50.40 | Cytokine | (68) |
| 24 | FYVE, RhoGEF and PH domain containing protein 3, FGD3 |
2COC | Wurst | -; 10.0 | PH domain-like barrel |
[50728] | Not yet assigned |
Signaling Protein | (69) | |
| 25 | Class delta GST | 1V2A | Wurst | -; 10.0 | GST C-terminal domain-like |
[47615] | Glutaredoxin | 3.40.30.10 | Transferase | (70) |
| 26 | PI-Pfui intein | 1DQ3 | Superfam | Hedgehog/intein (Hint) domain |
[51293] | Endonuclease - Pi- scei; Chain A, domain 1 |
2.170.16.10 | Hydrolase | (71) | |
| 27 | Galectin-1 | 1W6O | Superfam | Concanavalin A- like lectins/glucanases |
[49898] | Jelly Rolls | 2.60.120.200 | Lectin | (72) | |
| 28 | Isoamylase | 1BF2 | Libellula | 2.6; - | Immunoglobulin- like beta-sandwich |
[48725] | Immunoglobulins | 2.60.40.10 | Hydrolase | (73) |
| 29 | N-cadherin (neural) |
1OP4 | Libellula | 9.0; - | Immunoglobulin- like beta-sandwich |
[48725] | Not yet assigned | Cell Adhesion | (74) | |
| 30 | Plasminogen | 1KI0 | Libellula | 4.3; - | Kringle-like | [57439] | Plasminogen Kringle 4 |
2.40.20.10 | Hydrolase | (75) |
| 31 | CD69 | 1E8I | Libellula | -; 8.6 | C-type lectin-like | [56435] | Mannose-Binding Protein A, subunit A |
2.60.120.40 | Hematopoietic Cell Receptor | (76) |
| 32 | Tumor necrosis factor (TNF) |
2TNF | Libellula | -; 10.5 | TNF-like | [49841] | Jelly Rolls | 2.30.27.10 | Cytokine | (77) |
| 33 | minor coat protein g3p |
1G3P | Libellula | -; 11.7 | N-terminal domains of the minor coat protein g3p |
[50175] | Phage FD Coat Protein,Membrane penetration domain |
2.60.40.10 | Viral Protein | (78) |
| 34 | Immunoglobulin heavy chain |
1QFW | Libellula | -; 14.4 | Immunoglobulin- like beta-sandwich |
[48725] | Immunoglobulins | 2.10.60.10 | Immune System | (79) |
| 35 | TGF-beta type II receptor |
1KTZ | Libellula | -; 12.2 | Snake toxin-like | [57301] | CD59 | 3.10.200.10 | Cytokine/Cytokine Receptor | (80) |
| 36 | Carbonic anhydrase |
2ZNC | Loopp | 1.1; - | Carbonic anhydrase | [51068] | Carbonic Anhydrase II |
2.60.40.200 | Lyase | (81) |
| 37 | Copper chaperone for superoxide dismutase |
1DO5 | Loopp | 0.9; - | Immunoglobulin- like beta-sandwich |
[48725] | Immunoglobulin- like |
3.10.200.10 | Chaperone | (82) |
| 38 | Carbonic anhydrase |
1RJ6 | Loopp | 0.9; - | Carbonic anhydrase | [51068] | Carbonic Anhydrase II |
2.80.10.50 | Lyase | (83) |
| 39 | Winged bean albumin 1 |
1WBA | Loopp | 0.9; - | beta-Trefoil | [50352] | Trefoil (Acidic Fibroblast Growth Factor, subunit A) |
2.60.120.260 | Seed Storage Protein | (84) |
| 40 | Micromonospora sialidase |
1W8O | HHPred | 94; 97 | 6-bladed beta- propeller |
[50938] | Galactose-binding domain-like |
Hydrolase | (85) |