1. c.68.1 Nucleotide-diphospho-sugar transferases
Nucleotide-diphospho-sugar transferases 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214657; strand 6 is antiparallel to the rest
2cu2 d2cu2a2 A:83-99,101-108,188-193,193-206,205-218
2. d.128.1 Glutamine synthetase/guanido kinase
Glutamine synthetase/guanido kinase duplication: common core consists of two beta-alpha-beta2-alpha repeats
1r8g d1r8gb_ B:157-166,295-300,301-306,306-319,327-341
3. d.211.2 Plakin repeat repeats associate forming globular subdomains !
beta-hairpin-alpha-hairpin repeat multiple repeats of beta(2)-alpha(2) motif
1lm7 d1lm7b_ B:2284-2299,2300-2305,2306-2311,2311-2319,2322-2338
1lm7 d1lm7a_ A:2284-2299,2300-2305,2306-2311,2311-2319,2322-2338
4. a.86.1 Di-copper centre-containing domain duplication: contains two structural repeats !
Di-copper centre-containing domain multihelical
1hcy d1hcyf2 F:285-303,303-308,310-315,317-330,377-399
1hcy d1hcya2 A:285-303,303-308,310-315,317-330,377-399
1hcy d1hcyb2 B:285-303,303-308,310-315,317-330,377-399
1hcy d1hcyc2 C:285-303,303-308,310-315,317-330,377-399
1hcy d1hcyd2 D:285-303,303-308,310-315,317-330,377-399
1hcy d1hcye2 E:285-303,303-308,310-315,317-330,377-399
1hc1 d1hc1a2 A:285-303,303-308,310-315,317-330,377-399
5. d.144.1 Protein kinase-like (PK-like) shares functional and structural similarities with the ATP-grasp fold and PIPK !
Protein kinase-like (PK-like) consists of two alpha+beta domains, C-terminal domain is mostly alpha helical
1tqi d1tqia2 A:194-213,213-217,238-242,246-267,271-282
1tqm d1tqma2 A:194-213,213-217,238-242,246-267,271-282
1tqp d1tqpa2 A:194-213,213-217,238-242,246-267,271-282
1zyl d1zyla1 A:118-140,194-200,220-225,225-234,237-257
2pup d2pupa1 A:133-152,227-232,253-258,258-278,278-308
2pup d2pupb1 B:133-152,227-232,253-258,258-278,278-308
2olc d2olcb1 B:133-152,227-232,253-258,258-278,278-308
2pun d2punb1 B:133-152,227-232,253-258,258-278,278-308
2pu8 d2pu8a1 A:133-152,227-232,253-258,258-278,278-308
2olc d2olca1 A:133-152,227-232,253-258,258-278,278-308
2pui d2puib1 B:133-152,227-232,253-258,258-278,278-308
2pul d2pulb1 B:133-152,227-232,253-258,258-278,278-308
2pui d2puia1 A:133-152,227-232,253-258,258-278,278-308
2pul d2pula1 A:133-152,227-232,253-258,258-278,278-308
2pun d2puna1 A:133-152,227-232,253-258,258-278,278-308
6. e.7.1 Carbohydrate phosphatase
Carbohydrate phosphatase N-terminal domain is an alpha+beta, C-terminal domain is an alpha/beta with mixed beta-sheet
1inp d1inpa_ A:47-70,82-87,89-94,102-112,114-127
7. a.123.1 Nuclear receptor ligand-binding domain
Nuclear receptor ligand-binding domain multihelical; 3 layers or orthogonally packed helices
1l2j d1l2jb_ B:334-351,352-357,359-364,363-371,372-391
1q4x d1q4xa_ A:308-321,325-331,333-337,337-345,346-364
1nuo d1nuoa_ A:308-321,325-331,333-337,337-345,346-364
1nq2 d1nq2a_ A:308-321,325-331,333-337,337-345,346-364
1xzx d1xzxx_ X:308-321,325-331,333-337,337-345,346-364
1xb7 d1xb7a_ A:360-377,379-383,385-389,389-397,398-416
1y0x d1y0xx_ X:308-321,325-331,333-337,337-345,346-364
1nq0 d1nq0a_ A:308-321,325-331,333-337,337-345,346-364
1n46 d1n46b_ B:308-321,325-331,333-337,337-345,346-364
1nq1 d1nq1a_ A:308-321,325-331,333-337,337-345,346-364
1xdk d1xdkb_ B:257-270,274-280,282-286,286-294,295-313
1xdk d1xdkf_ F:257-270,274-280,282-286,286-294,295-313
4lbd d4lbda_ A:266-279,283-289,291-295,295-303,304-322
3lbd d3lbda_ A:266-279,283-289,291-295,295-303,304-322
1dkf d1dkfb_ B:264-277,281-287,289-293,293-301,302-320
1fcz d1fcza_ A:266-279,283-289,291-295,295-303,304-322
1fd0 d1fd0a_ A:266-279,283-289,291-295,295-303,304-322
2lbd d2lbda_ A:266-279,283-289,291-295,295-303,304-322
1exa d1exaa_ A:266-279,283-289,291-295,295-303,304-322
1xap d1xapa_ A:257-270,274-280,282-286,286-294,295-313
1exx d1exxa_ A:266-279,283-289,291-295,295-303,304-322
1fcy d1fcya_ A:266-279,283-289,291-295,295-303,304-322
1fcx d1fcxa_ A:266-279,283-289,291-295,295-303,304-322
8. a.118.8 TPR-like
alpha-alpha superhelix multihelical; 2 (curved) layers: alpha/alpha; right-handed superhelix
3ckb d3ckba1 A:145-171,172-176,184-188,188-207,219-239
3ckc d3ckca1 A:145-171,172-176,184-188,188-207,219-239
3ck7 d3ck7c1 C:145-171,172-176,184-188,188-207,219-239
9. e.72.1 SSO1389-like
SSO1389-like 2 domains; d1: [alpha/beta, central parallel beta-sheet of 6 strands, order 321456, Rossmann-like]; d2: [alpha+beta, cluster of helices and a small 4-stranded beta-sheet]
2i71 d2i71a1 A:129-153,155-163,176-185,185-200,266-283
10. d.153.1 N-terminal nucleophile aminohydrolases (Ntn hydrolases) N-terminal residue provides two catalytic groups, nucleophile and proton donor !
Ntn hydrolase-like 4 layers: alpha/beta/beta/alpha; has an unusual sheet-to-sheet packing
2i3o d2i3oc1 C:35-52,59-68,71-78,110-124,127-142
2i3o d2i3oa1 A:35-52,59-68,71-78,110-124,127-142
2i3o d2i3od1 D:35-52,59-68,71-78,110-124,127-142
2i3o d2i3ob1 B:35-52,59-68,71-78,110-124,127-142
2nlz d2nlzc1 C:46-63,70-79,80-88,120-134,137-152
2nlz d2nlzd1 D:46-63,70-79,80-88,120-134,137-152
2nlz d2nlzb1 B:46-63,70-79,80-88,120-134,137-152
2e0x d2e0x.2 C:71-88,95-104,106-114,148-162,165-180
2e0w d2e0wa1 A:71-88,95-104,106-114,148-162,165-180
2nlz d2nlza1 A:46-63,70-79,80-88,120-134,137-152
2dbw d2dbw.2 C:71-88,95-104,106-114,148-162,165-180
2e0y d2e0y.2 C:71-88,95-104,106-114,148-162,165-180
2dg5 d2dg5.2 C:71-88,95-104,106-114,148-162,165-180
2e0w d2e0wb1 B:71-88,95-104,106-114,148-162,165-180
2e0x d2e0x.1 A:71-88,95-104,106-114,148-162,165-180
2dg5 d2dg5.1 A:71-88,95-104,106-114,148-162,165-180
2e0y d2e0y.1 A:71-88,95-104,106-114,148-162,165-180
2dbx d2dbx.2 C:71-88,95-104,106-114,148-162,165-180
2dbw d2dbw.1 A:71-88,95-104,106-114,148-162,165-180
2dbu d2dbu.1 A:71-88,95-104,106-114,148-162,165-180
2dbu d2dbu.2 C:71-88,95-104,106-114,148-162,165-180
2dbx d2dbx.1 A:71-88,95-104,106-114,148-162,165-180
2nqo d2nqo.1 A:60-77,84-93,95-103,137-151,154-169
11. a.100.1 6-phosphogluconate dehydrogenase C-terminal domain-like N-terminal domain is Rossmann-fold with a family-specific C-terminal extension !
6-phosphogluconate dehydrogenase C-terminal domain-like multihelical; common core is formed around two long antiparallel helices related by (pseudo) twofold symmetry
1bg6 d1bg6a1 A:84-96,130-136,158-165,188-196,291-313
1bg6 d1bg6a1 A:113-126,130-136,158-165,188-196,291-313
2ofp d2ofpa1 A:100-107,111-119,133-142,168-191,256-272
1ks9 d1ks9a1 A:100-107,111-120,133-142,168-191,256-272
1yjq d1yjqa1 A:100-107,111-119,133-142,168-191,256-272
1qmg d1qmga1 A:226-237,243-253,272-281,307-342,391-409
1qmg d1qmgb1 B:226-237,243-253,272-281,307-342,391-409
12. c.95.1 Thiolase-like
Thiolase-like consists of two similar domains related by pseudo dyad; duplication ! 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32451; strand 5 is antiparallel to the rest
1u0m d1u0ma1 A:136-156,157-168,189-200,291-302,304-320
1u0m d1u0mb1 B:136-156,157-168,189-200,291-302,304-320
1d6i d1d6ib1 B:162-182,185-194,216-226,324-335,337-357
13. a.102.1 Six-hairpin glycosidases
alpha/alpha toroid multihelical; up to seven alpha-hairpins are arranged in closed circular array; there may be sequence similarities between different superfamilies
2fba d2fbaa1 A:362-384,385-391,415-421,423-448,471-492
1ayx d1ayxa_ A:362-384,385-391,415-421,423-448,471-492
2f6d d2f6da1 A:362-384,385-391,415-421,423-448,471-492
14. c.55.3 Ribonuclease H-like consists of one domain of this fold !
Ribonuclease H-like motif 3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
1uoc d1uoca_ A:60-77,76-88,98-104,137-149,162-176
15. c.7.1 PFL-like glycyl radical enzymes duplication: the N- and C-terminal halves have similar topologies !
PFL-like glycyl radical enzymes contains: barrel, closed; n=10, S=10; accommodates a hairpin loop inside the barrel
1hk8 d1hk8a_ A:83-91,90-95,96-101,104-124,131-155
1h7b d1h7ba_ A:83-91,90-95,96-101,104-124,131-155
1h7a d1h7aa_ A:83-91,91-95,96-100,104-124,131-155
16. c.1.13 Malate synthase G
TIM beta/alpha-barrel contains parallel beta-sheet barrel, closed; n=8, S=8; strand order 12345678 ! the first seven superfamilies have similar phosphate-binding sites
1p7t d1p7tb_ B:588-614,617-623,625-631,631-649,707-722
1p7t d1p7ta_ A:588-614,617-623,625-631,631-649,707-722
1n8i d1n8ia_ A:590-616,619-625,627-633,633-651,709-727
1n8w d1n8wa_ A:590-616,619-625,627-633,633-651,709-727
2gq3 d2gq3b1 B:590-616,619-625,627-633,633-651,709-726
1n8w d1n8wb_ B:590-616,619-625,627-633,633-651,709-727
2gq3 d2gq3a1 A:590-616,619-625,627-633,633-651,709-727
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 1022 (enumeration index: query2391) of S5
3a75 A:69-86,93-103,104-113,148-162,165-180
3a75 C:69-86,93-103,104-113,148-162,165-180
2x60 A:85-98,102-108,192-196,196-209,208-218
2x60 B:85-98,102-108,192-196,196-209,208-218
2xrf A:29-36,38-42,43-47,51-59,117-136
2xrf B:29-36,38-42,43-47,51-59,117-136
2fa3 A:115-133,140-150,160-172,314-325,327-344
2z8k C:71-88,95-104,106-114,148-162,165-180
2z8k A:71-88,95-104,106-114,148-162,165-180
3fnm A:60-77,84-93,95-103,137-151,154-169
3fnm C:60-77,84-93,95-103,137-151,154-169
3lvw A:286-298,530-535,544-549,549-556,589-605
3ku4 D:22-29,30-35,36-41,44-52,110-129
3ig5 A:286-298,530-535,544-549,549-556,589-605
3c7d B:120-130,135-142,164-174,199-208,323-345
2pin B:308-321,325-331,333-337,337-345,346-364
3q3c A:98-113,114-123,133-139,162-196,240-259
3c7a A:120-130,135-142,164-174,199-208,323-345
3hl6 B:75-89,89-93,95-99,99-111,151-166
2r6f B:887-895,895-900,908-916,916-924,926-949
2r6f A:887-895,895-900,908-916,916-924,926-949
2gwc E:173-196,244-250,383-387,393-411,471-486
2gwc B:173-196,244-250,383-387,393-411,471-486
2gwc G:173-196,244-250,383-387,393-411,471-486
2gwc D:173-196,244-250,383-387,393-411,471-486
2gwc C:173-196,244-250,383-387,393-411,471-486
2gwc A:173-196,244-250,383-387,393-411,471-486
2gwc F:173-196,244-250,383-387,393-411,471-486
2gwc H:173-196,244-250,383-387,393-411,471-486
3c7c B:120-130,135-142,164-174,199-208,323-345
3imy A:308-321,325-331,333-337,337-345,346-364
3iqd B:120-130,135-142,164-174,199-208,323-345
3gws X:308-321,325-331,333-337,337-345,346-364
3i83 A:107-117,120-128,144-151,178-201,267-283
3i83 B:107-117,120-128,144-151,178-201,267-283
3gwj C:308-332,332-336,339-343,345-358,409-431
3gwj E:308-332,332-336,339-343,345-358,409-431
3gwj F:308-332,332-336,339-343,345-358,409-431
3gwj D:308-332,332-336,339-343,345-358,409-431
3gwj B:308-332,332-336,339-343,345-358,409-431
3gwj A:308-332,332-336,339-343,345-358,409-431
2xsm E:21-42,48-52,57-61,63-71,75-87
2xsm I:21-42,49-53,57-61,63-71,75-88
2ckp A:221-238,299-305,333-339,338-352,371-388
2x5s A:85-98,101-108,192-196,196-209,208-218
2x5s B:85-98,101-108,192-196,196-209,208-218
3zqj E:904-911,912-921,924-933,933-941,943-953
3zqj C:904-912,912-920,924-933,933-941,943-953
3zqj B:904-911,912-920,924-933,933-941,943-953
3zqj A:904-911,912-920,924-933,933-941,943-953
3zqj D:904-911,912-920,924-933,933-941,943-953
2x65 B:85-98,101-108,192-196,196-209,208-218
2x65 A:85-98,102-108,192-196,196-209,208-218
3pih A:867-874,875-881,890-896,896-904,906-916
3g9k L:71-88,95-104,105-113,130-144,147-162
3g9k D:71-88,95-104,105-113,130-144,147-162
2qh5 B:87-100,103-110,188-192,192-205,204-218
3ig8 A:286-298,530-535,544-549,549-556,589-605
3iyg Q:8-31,37-42,46-51,52-61,64-82
2v36 C:69-86,93-103,104-113,148-162,165-180
2v36 A:69-86,93-102,105-113,148-162,165-180
1r6g A:308-321,325-331,333-337,337-345,346-364
3lvv A:286-298,530-535,544-549,549-556,589-605
3obb A:98-113,115-123,133-139,162-196,240-259
2qmc A:60-77,84-93,95-103,137-151,154-169
2qmc C:60-77,84-93,95-103,137-151,154-169
2h79 A:254-267,271-277,279-283,283-291,292-310
3eut B:150-173,176-186,211-222,326-337,339-353
3eut D:150-173,176-186,211-222,326-337,339-353
3eut A:150-173,176-186,211-222,326-337,339-353
3kmz B:264-277,281-287,289-293,293-301,302-320
3kmz A:264-277,281-287,289-293,293-301,302-320
2pyw A:136-155,232-237,258-263,263-286,292-322
2pyw B:136-156,232-237,258-263,263-286,292-322
3p0e E:29-36,37-42,43-48,51-59,117-136
3hn2 C:103-115,118-125,139-149,176-199,268-284
3g79 B:150-167,173-180,195-202,227-260,291-309
3g79 A:150-167,173-180,194-202,227-260,291-309
3nbq A:23-30,32-36,37-41,45-53,111-130
3kmr A:264-277,281-287,289-293,293-301,302-320
3att A:158-179,243-248,270-275,275-298,307-320
2wya A:164-182,189-199,209-221,368-379,381-398
2wya D:164-182,189-199,209-221,368-379,381-398
2wya C:164-182,189-199,209-221,368-379,381-398
2wya B:164-182,189-199,209-221,368-379,381-398
2h77 A:254-267,271-277,279-283,283-291,292-310
2p8u B:127-145,152-162,172-184,331-342,344-360
2p8u A:127-145,152-162,172-184,331-342,344-360
3d57 B:308-321,325-331,333-337,337-345,346-364
3ats A:158-179,243-248,270-275,275-298,307-320
2yz2 A:197-205,206-213,214-221,221-229,235-248
2yz2 B:197-205,206-213,214-221,221-229,235-249
3cky B:101-116,116-126,136-142,165-199,237-256
3cky A:101-116,116-126,136-142,165-199,237-256
3fr8 A:226-237,243-252,273-281,307-342,391-409
3fr8 B:226-237,243-253,272-281,307-342,391-409
3euo B:150-173,176-186,211-222,326-337,339-353
1y9r B:805-823,826-830,832-836,836-844,845-863
3fr7 A:226-237,244-253,273-283,307-324,391-409
3fi8 A:198-220,282-287,308-313,313-327,346-363
3csv A:105-126,182-186,214-218,218-229,235-251
3a9e B:264-277,281-287,289-293,293-301,302-320
3jzc A:308-321,325-331,333-337,337-345,346-364
2x5z A:85-98,101-108,192-196,196-209,208-218
2x5z B:85-98,102-108,192-196,196-209,208-218
2qm6 C:60-77,84-93,95-103,137-151,154-169
2qm6 A:60-77,84-93,95-103,137-151,154-169
2z8j C:71-88,95-104,106-114,148-162,165-180
2z8j A:71-88,95-104,106-114,148-162,165-180
3euf B:23-30,32-36,37-41,45-53,111-130
3ego A:99-109,112-122,135-145,171-194,258-274
3ego B:99-110,112-122,135-145,171-194,258-274
3jzb A:254-267,271-277,279-283,283-291,292-310
3ga9 L:71-88,95-104,105-113,130-144,147-162
3e1h A:150-173,176-186,211-222,326-337,339-354
3ixv M:262-280,280-285,287-292,293-307,354-376
3ixv L:262-280,280-285,287-292,293-307,354-376
3ixv A:262-280,280-285,287-292,293-307,354-376
3ixv K:262-280,280-285,287-292,296-307,354-376
3ixv G:262-280,280-285,287-292,293-307,354-376
3ixv C:262-280,280-285,287-292,293-307,354-376
3ixv E:262-280,280-285,287-292,296-307,354-376
3ixv H:262-280,280-285,287-292,293-307,354-376
3ixv D:262-280,280-285,287-292,293-307,354-376
3euq C:150-173,176-186,211-222,326-337,339-353
3euq A:150-173,176-186,211-222,326-337,339-353
3euq B:150-173,176-186,211-222,326-337,339-353
2z8i C:71-88,95-104,106-114,148-162,165-180
2z8i A:71-88,95-104,106-114,148-162,165-180
2nqo C:60-77,84-93,95-103,137-151,154-169
1hc1 F:285-303,303-308,310-315,317-330,377-399
1hc1 C:285-303,303-308,310-315,317-330,377-399
1hc1 D:285-303,303-308,310-315,317-330,377-399
1hc1 B:285-303,303-308,310-315,317-330,377-399
1hc1 E:285-303,303-308,310-315,317-330,377-399