1. d.3.1 Cysteine proteinases the constitute families differ by insertion into and circular permutation of the common catalytic core made of one alpha-helix and 3-strands of beta-sheet !
Cysteine proteinases consists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn
1g0d d1g0da4 A:183-195,201-212,211-227,271-287,350-356
1kv3 d1kv3a4 A:186-200,206-217,216-232,276-292,353-360
1kv3 d1kv3d4 D:186-200,206-217,216-232,276-292,353-360
1kv3 d1kv3b4 B:186-200,206-217,216-232,276-292,353-360
1kv3 d1kv3e4 E:186-200,206-217,216-232,276-292,353-360
1kv3 d1kv3f4 F:186-200,206-217,216-232,276-292,353-360
1kv3 d1kv3c4 C:186-200,206-217,216-232,276-292,353-360
2q3z d2q3za4 A:186-200,206-217,216-230,276-292,353-358
1nud d1nudb4 B:181-195,201-212,211-224,271-287,348-354
1nuf d1nufa4 A:181-195,201-212,211-224,271-287,348-354
1l9m d1l9ma4 A:181-195,201-212,211-224,271-287,348-354
1nud d1nuda4 A:181-195,201-212,211-224,271-287,348-354
1l9m d1l9mb4 B:181-195,201-212,211-224,271-287,348-354
1nug d1nugb4 B:181-195,201-212,211-224,271-287,348-354
1l9n d1l9nb4 B:181-195,201-212,211-224,271-287,348-354
1l9n d1l9na4 A:181-195,201-212,211-224,271-287,348-354
1nug d1nuga4 A:181-195,201-212,211-224,271-287,348-354
2q3z d2q3za4 A:186-200,206-217,216-230,276-292,294-305
2. a.98.1 R1 subunit of ribonucleotide reductase, N-terminal domain
R1 subunit of ribonucleotide reductase, N-terminal domain multihelical consists of two all-alpha subdomains ! subdomain 1 (residues 10-100) is a 4-helical bundle
4r1r d4r1rb1 B:18-31,37-49,54-70,74-95,649-656
4r1r d4r1rc1 C:18-31,37-49,54-70,74-95,649-656
4r1r d4r1ra1 A:18-31,37-49,54-70,74-95,649-656
3r1r d3r1rc1 C:18-31,37-49,54-70,74-95,649-656
3r1r d3r1ra1 A:18-31,37-49,54-70,74-95,649-656
3r1r d3r1rb1 B:18-31,37-49,54-70,74-95,649-656
5r1r d5r1rc1 C:18-31,37-49,54-70,74-95,649-656
2r1r d2r1ra1 A:18-31,37-49,54-70,74-95,649-656
2r1r d2r1rb1 B:18-31,37-49,54-70,74-95,649-656
2r1r d2r1rc1 C:18-31,37-49,54-70,74-95,649-656
5r1r d5r1rb1 B:18-31,37-49,54-70,74-95,649-656
7r1r d7r1rc1 C:18-31,37-49,54-70,74-95,649-656
5r1r d5r1ra1 A:18-31,37-49,54-70,74-95,649-656
7r1r d7r1ra1 A:18-31,37-49,54-70,74-95,649-656
7r1r d7r1rb1 B:18-31,37-49,54-70,74-95,649-656
1r1r d1r1rb1 B:18-31,37-49,54-70,74-95,649-656
1r1r d1r1ra1 A:18-31,37-49,54-70,74-95,649-656
6r1r d6r1rc1 C:18-31,37-49,54-70,74-95,649-656
1rlr d1rlra1 A:18-31,37-50,54-70,74-95,649-656
1r1r d1r1rc1 C:18-31,37-49,54-70,74-95,649-656
6r1r d6r1rb1 B:18-31,37-49,54-70,74-95,649-656
6r1r d6r1ra1 A:18-31,37-49,54-70,74-95,649-656
3. a.96.1 DNA-glycosylase
DNA-glycosylase multihelical; consists of two all-alpha domains
1rrs d1rrsa1 A:35-47,50-66,75-84,88-107,263-268
1rrq d1rrqa1 A:35-47,50-66,75-84,88-107,263-268
1vrl d1vrla1 A:35-47,50-66,75-84,88-107,263-268
4. e.8.1 DNA/RNA polymerases "palm" domain has a ferredoxin-like fold, related to that of an adenylyl cyclase domain !
DNA/RNA polymerases divided into morphological domains including "palm", "thumb" and "fingers"; the catalytic "palm" domain is conserved to all members
1n38 d1n38a_ A:224-244,246-264,265-285,358-372,783-788
1muk d1muka_ A:224-244,246-264,265-285,358-372,783-788
1n1h d1n1ha_ A:224-244,246-264,265-285,358-372,783-788
1mwh d1mwha_ A:224-244,246-264,265-285,358-372,783-788
1n35 d1n35a_ A:224-244,246-264,265-285,358-372,783-788
2pi5 d2pi5a1 A:72-96,110-129,133-152,205-225,754-763
1qln d1qlna_ A:72-96,110-129,133-152,205-225,754-763
1cez d1ceza_ A:72-96,110-129,133-152,205-225,754-763
2pi4 d2pi4a1 A:72-96,110-129,133-152,205-225,754-763
5. i.7.1 Reovirus components
Reovirus components
1uon d1uona_ A:224-244,246-264,265-285,358-372,783-788
6. b.81.1 Trimeric LpxA-like enzymes superhelical turns are made of three short strands; duplication: the sequence hexapeptide repeats correspond to individual strands !
Single-stranded left-handed beta-helix superhelix turns are made of parallel beta-strands and (short) turns
1sst d1sstb_ B:55-71,70-89,101-120,121-137,137-143
1ssm d1ssmc_ C:55-71,70-89,101-120,121-137,137-143
1sst d1sstc_ C:55-71,70-89,101-120,121-137,137-143
1ssm d1ssme_ E:55-71,70-89,101-120,121-137,137-143
1ssm d1ssma_ A:55-71,70-89,101-120,121-137,137-143
1ssm d1ssmd_ D:55-71,70-89,101-120,121-137,137-143
1ssm d1ssmf_ F:55-71,70-89,101-120,121-137,137-143
1ssm d1ssmb_ B:55-71,70-89,101-120,121-137,137-143
1sst d1ssta_ A:55-71,70-89,101-120,121-137,137-143
1t3d d1t3da_ A:59-75,74-93,105-124,125-141,141-147
1s80 d1s80f_ F:55-71,70-89,101-120,121-137,137-143
1s80 d1s80b_ B:55-71,70-89,101-120,121-137,137-143
1s80 d1s80c_ C:55-71,70-89,101-120,121-137,137-143
1ssq d1ssqd_ D:55-71,70-89,101-120,121-137,137-143
7. c.108.1 HAD-like usually contains an insertion (sub)domain after strand 1 !
HAD-like 3 layers: a/b/a; parallel beta-sheet of 6 strands, order 321456
1l8l d1l8la_ A:29-39,40-54,57-70,72-83,134-139
1l8l d1l8lb_ B:29-39,40-52,57-70,72-83,134-139
1l8o d1l8ob_ B:29-39,40-52,57-70,72-83,134-139
1l8o d1l8oa_ A:29-39,40-52,57-70,72-83,134-139
2cn1 d2cn1a1 A:55-63,67-87,91-114,116-127,180-185
1l8l d1l8la_ A:29-39,40-54,57-70,112-124,134-139
1l8o d1l8oa_ A:29-39,40-52,57-70,112-124,134-139
1l8o d1l8ob_ B:29-39,40-52,57-70,112-124,134-139
8. a.234.1 Hypothetical protein MPN330
Hypothetical protein MPN330 multihelical; consists of three different 4-helical bundles
1td6 d1td6a_ A:77-101,122-132,138-151,155-169,173-183
9. d.334.1 IlvD/EDD N-terminal domain-like
IlvD/EDD N-terminal domain-like contains a large cluster of helices and a mixed beta-sheet of 4 strands; order 2134, strands 3 and 4 are parallel
2gp4 d2gp4a2 A:2-17,283-298,300-315,319-331,419-426
10. a.111.1 Acid phosphatase/Vanadium-dependent haloperoxidase
Acid phosphatase/Vanadium-dependent haloperoxidase multihelical; core: 5-helical bundle; binds cofactor at the beginning of third helix
1qhb d1qhba_ A:375-403,483-501,529-549,552-578,584-589
1qhb d1qhbb_ B:375-403,483-501,529-549,552-578,584-589
1up8 d1up8a_ A:376-404,484-502,530-550,553-579,585-590
1up8 d1up8d_ D:376-404,484-502,530-550,553-579,585-590
1up8 d1up8b_ B:376-404,484-502,530-550,553-579,585-590
1up8 d1up8c_ C:376-404,484-502,530-550,553-579,585-590
1qhb d1qhbc_ C:375-403,483-501,529-549,552-579,584-589
1qhb d1qhbd_ D:375-403,483-501,529-549,552-579,584-589
1qhb d1qhbe_ E:375-403,483-501,529-549,552-579,584-589
1qhb d1qhbf_ F:375-403,483-501,529-549,552-579,584-589
1qi9 d1qi9a_ A:319-346,416-434,464-484,487-513,518-524
1qi9 d1qi9b_ B:319-346,416-434,464-484,487-513,518-524
11. e.3.1 beta-lactamase/transpeptidase-like
beta-lactamase/transpeptidase-like contains a cluster of helices and an alpha+beta sandwich
1xa7 d1xa7a_ A:61-73,120-132,153-167,172-184,207-218
1xa1 d1xa1b_ B:57-73,120-132,153-167,172-184,204-218
1xkz d1xkzb_ B:387-403,450-462,483-497,502-514,534-548
12. a.7.12 PhoU-like duplication: consists of two sequence each repeats adopting this fold !
Spectrin repeat-like 3 helices; bundle, closed, left-handed twist; up-and-down
1sum d1sumb_ B:73-111,116-140,141-174,173-210,212-217
1sum d1sumb_ B:3-37,116-140,141-174,173-210,212-217
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1195 (enumeration index: query224.2382) of S5
2j3v A:14-33,34-47,46-63,76-93,181-190
2xo5 A:18-31,37-49,54-70,74-95,649-656
2xo5 B:18-31,37-49,54-70,74-95,649-656
2xo5 C:18-31,37-49,54-70,74-95,649-656
3fsp A:35-47,50-66,75-84,88-107,263-268
2wn8 A:25-39,39-53,52-63,74-91,182-189
2xo4 C:18-31,37-49,54-70,74-95,649-656
2xo4 B:18-31,37-49,54-70,74-95,649-656
2xo4 A:18-31,37-49,54-70,74-95,649-656
3kd3 A:16-27,29-46,49-62,64-76,127-132
3p1b A:57-81,81-96,127-146,147-163,163-169
3hnc A:14-27,35-47,52-72,71-91,631-638
3hnc B:14-27,35-47,52-72,71-91,632-638
2xak A:18-31,37-49,54-70,74-95,649-656
2xak C:18-31,37-49,54-70,74-95,649-656
2xak B:18-31,37-49,54-70,74-95,649-656
3e3j C:73-96,110-130,133-152,205-225,754-763
3e3j B:73-96,110-130,133-151,205-225,754-763
3hnf A:14-27,35-47,52-72,71-90,631-638
3hnf B:14-27,35-48,52-72,71-91,632-638
2xav C:18-31,37-49,54-70,74-95,650-656
2xav A:18-31,37-49,54-70,74-95,649-656
2xav B:18-31,37-49,54-70,74-95,650-656
3mdn B:121-130,130-138,141-154,158-178,182-192
3mdn D:121-130,130-138,141-154,158-178,182-192
3mdn A:121-130,130-138,141-154,158-178,182-192
3mdn C:121-130,130-138,141-154,158-178,182-192
3ly6 A:186-200,206-217,216-230,276-292,353-361
3ly6 C:186-200,206-217,216-230,276-292,353-361
3ly6 B:186-200,206-217,216-230,276-292,353-361
2xaw A:18-31,37-49,54-70,74-95,649-656
2xaw B:18-31,37-49,54-70,74-95,649-656
2xaw C:18-31,37-49,54-70,74-95,649-656
2xap A:18-31,37-49,54-70,74-95,649-656
2xap C:18-31,37-49,54-70,74-95,649-656
2xap B:18-31,37-49,54-70,74-95,649-656
2xax A:18-31,37-49,54-70,74-95,649-656
2xax B:18-31,37-49,54-70,74-95,650-656
2xax C:18-31,37-49,54-70,74-95,649-656
3q1x A:57-81,81-96,127-146,147-163,163-169
3g0q A:35-47,50-66,75-84,88-107,263-268
3e2e A:73-96,110-130,133-152,205-225,754-763
3m1y D:17-27,28-41,45-58,61-72,113-121
3m1y C:17-27,28-42,45-58,61-72,117-121
3m1y B:17-27,28-42,45-58,61-72,117-121
3m1y A:17-27,28-36,45-58,61-72,117-121
2x0x A:18-31,37-49,54-70,74-95,649-656
2x0x B:18-31,37-49,54-70,74-95,650-656
2x0x C:18-31,37-49,54-70,74-95,649-656
3qo7 A:214-223,223-231,246-256,374-382,382-386
2xay A:18-31,37-49,54-70,74-95,649-656
2xay B:18-31,37-49,54-70,74-95,649-656
2xay C:18-31,37-49,54-70,74-95,649-656
1zyz A:17-27,35-44,52-72,71-91,637-642
1zyz B:17-27,35-44,52-72,71-91,636-642
2r7w A:200-217,219-237,236-255,315-333,679-684
2wn5 A:24-39,39-53,52-63,74-91,181-190
3gvd I:59-75,74-93,105-124,125-141,141-147
3gvd G:59-75,74-93,105-124,125-141,141-147
3gvd B:59-75,74-93,105-124,125-141,141-147
3qo5 A:214-223,223-231,246-256,374-382,382-386
3p47 A:57-81,81-96,127-146,147-163,163-169
3f1x A:64-94,108-123,154-173,174-190,190-196
3hnd A:14-27,35-47,52-72,71-90,631-638
3hnd B:14-27,35-47,52-72,71-90,633-638
2j3x A:14-33,34-47,46-63,76-93,181-190
3fsq A:35-47,50-66,75-84,88-107,263-268
2xaz C:18-31,37-49,54-70,74-95,649-656
2xaz A:18-31,37-49,54-70,74-95,649-656
2xaz B:18-31,37-49,54-70,74-95,649-656