1. 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
1p4k d1p4kc_ C:305-311,311-323,330-346,576-582,583-589
9gaa d9gaac_ C:305-311,311-323,330-346,576-582,583-589
9gac d9gacc_ C:305-311,311-323,330-346,576-582,583-589
9gaa d9gaaa_ A:5-11,11-23,30-46,276-282,283-289
9gac d9gaca_ A:5-11,11-23,30-46,276-282,283-289
1p4v d1p4vc_ C:305-311,311-328,330-346,576-582,583-589
1p4k d1p4ka_ A:5-11,11-28,30-46,276-282,283-289
9gaf d9gafc_ C:305-311,311-328,330-346,576-582,583-589
1p4v d1p4va_ A:5-11,11-28,30-46,276-282,283-289
9gaf d9gafa_ A:5-11,11-28,30-46,276-282,283-289
2. c.1.9 Metallo-dependent hydrolases the beta-sheet barrel is similarly distorted and capped by a C-terminal helix ! has transition metal ions bound inside the barrel !
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
1j79 d1j79a_ A:4-11,273-286,287-297,310-318,342-346
2eg6 d2eg6a1 A:4-11,273-286,287-297,310-318,342-346
1xge d1xgea1 A:5-11,273-286,287-297,310-318,342-346
1j79 d1j79b_ B:5-11,273-286,287-297,310-318,342-346
1xge d1xgeb1 B:5-11,273-286,287-297,310-318,342-346
2eg7 d2eg7a1 A:5-11,273-286,287-297,310-318,342-346
2eg8 d2eg8b1 B:5-11,273-286,287-297,310-318,342-346
2eg7 d2eg7b1 B:5-11,273-286,287-297,310-318,342-346
2eg6 d2eg6b1 B:5-11,273-286,287-297,310-318,342-346
2eg8 d2eg8a1 A:5-11,273-286,287-297,310-318,342-346
1gkq d1gkqb2 B:49-54,340-356,359-369,391-397,424-432
1kcx d1kcxb2 B:63-67,360-373,376-386,407-415,440-449
2ftw d2ftwa2 A:56-61,353-366,369-379,400-408,433-442
1gkp d1gkpf2 F:49-54,340-356,359-376,391-397,424-432
1gkp d1gkpb2 B:49-54,340-356,359-376,391-397,424-432
1gkp d1gkpe2 E:49-54,340-356,359-376,391-397,424-432
1k1d d1k1df2 F:48-53,344-357,360-370,392-399,424-433
2ics d2icsa2 A:50-55,285-297,299-316,329-340,354-365
1nfg d1nfga2 A:47-52,339-354,357-374,389-396,421-430
1nfg d1nfgb2 B:47-52,339-354,357-374,389-396,421-430
1nfg d1nfgc2 C:47-52,339-354,357-374,389-396,421-430
1yny d1ynyb2 B:48-53,344-357,360-370,392-399,424-433
1nfg d1nfgd2 D:47-52,339-354,357-374,388-396,421-430
1gkp d1gkpc2 C:49-54,340-357,359-376,391-397,424-432
1yny d1ynya2 A:48-53,344-357,360-370,392-399,424-433
1gkp d1gkpa2 A:49-54,340-357,359-376,391-397,424-432
1xrt d1xrtb2 B:51-56,329-341,344-361,374-381,406-415
1k1d d1k1dg2 G:48-53,344-357,360-377,392-399,424-433
1k1d d1k1da2 A:48-53,344-357,360-377,392-399,424-433
1k1d d1k1dh2 H:48-53,344-357,360-377,392-399,424-433
1k1d d1k1dd2 D:48-53,344-357,360-377,392-399,424-433
1k1d d1k1db2 B:48-53,344-357,360-377,392-399,424-433
1k1d d1k1dc2 C:48-53,344-357,360-377,392-399,424-433
1k1d d1k1de2 E:48-53,344-357,360-377,392-399,424-433
1po9 d1po9a2 A:58-62,306-322,324-333,354-361,363-371
1gkr d1gkrd2 D:49-54,336-353,356-373,388-395,420-429
1gkr d1gkrc2 C:49-54,336-353,356-373,388-395,420-429
1gkr d1gkrb2 B:49-54,336-353,356-373,388-395,420-429
1gkr d1gkra2 A:49-54,336-353,356-373,388-395,420-429
1pok d1poka2 A:58-63,306-322,324-333,355-361,363-371
1pok d1pokb2 B:58-62,306-322,324-333,354-361,363-371
1xrf d1xrfa2 A:51-56,325-341,344-361,374-381,406-415
1po9 d1po9b2 B:58-62,306-322,324-333,355-361,363-371
1o12 d1o12b2 B:38-44,294-307,309-319,340-346,348-356
1xrt d1xrta2 A:51-56,325-341,344-361,374-381,406-415
1poj d1poja2 A:58-62,306-322,324-333,355-361,363-371
1poj d1pojb2 B:58-62,306-322,324-333,355-361,363-371
1gkq d1gkqc2 C:49-54,343-356,359-369,391-397,424-432
1gkq d1gkqa2 A:49-54,343-356,359-369,391-397,424-432
1gkq d1gkqd2 D:49-54,343-356,359-369,391-397,424-432
1onx d1onxa2 A:58-62,306-322,324-341,354-361,363-371
1kcx d1kcxa2 A:63-68,360-373,376-386,407-414,441-449
1o12 d1o12a2 A:39-43,294-307,309-326,340-346,348-356
1gkp d1gkpd2 D:49-54,343-356,359-376,391-397,424-432
1onw d1onwb2 B:58-62,306-322,329-341,354-361,363-371
1onw d1onwa2 A:58-62,306-322,329-341,354-361,363-371
1onx d1onxb2 B:58-62,306-322,329-341,354-361,363-371
2p50 d2p50c2 C:49-54,312-325,327-344,358-365,367-375
1ymy d1ymya2 A:49-54,312-325,327-344,358-365,367-375
1ymy d1ymyb2 B:49-54,312-325,327-344,358-365,367-375
2p53 d2p53b2 B:49-54,312-325,327-344,358-365,367-375
2p50 d2p50a2 A:49-54,312-325,327-344,358-365,367-375
2p50 d2p50b2 B:49-54,312-325,327-344,358-365,367-375
1yrr d1yrrb2 B:49-54,312-325,327-344,358-365,367-375
1yrr d1yrra2 A:49-54,312-325,327-344,358-365,367-375
2p53 d2p53a2 A:49-54,312-325,327-344,358-365,367-375
2p50 d2p50d2 D:49-54,312-325,327-344,358-365,367-375
3. d.65.1 Hedgehog/DD-peptidase zinc-binding motif !
Hedgehog/DD-peptidase alpha-beta(2)-alpha-beta(2); 2 layers: alpha/beta
2ibg d2ibge1 E:105-109,159-178,214-229,231-236,240-245
2ibg d2ibgh1 H:105-109,159-178,214-229,231-236,240-245
1vhh d1vhha_ A:46-50,100-119,155-170,172-177,181-186
2ibg d2ibgg1 G:105-109,159-178,214-229,231-236,240-245
4. d.14.1 Ribosomal protein S5 domain 2-like
Ribosomal protein S5 domain 2-like core: beta(3)-alpha-beta-alpha; 2 layers: alpha/beta; left-handed crossover
1fi4 d1fi4a1 A:32-39,141-154,153-162,163-170,177-185
1k47 d1k47e1 E:21-29,127-143,148-157,158-165,188-194
1k47 d1k47c1 C:21-29,127-143,148-157,158-165,188-194
1k47 d1k47d1 D:21-29,127-143,148-157,158-165,188-194
1k47 d1k47f1 F:21-29,127-143,148-157,158-165,188-194
1k47 d1k47a1 A:21-29,127-143,148-157,158-165,188-194
1kkh d1kkha1 A:25-32,137-154,157-167,168-174,175-180
1k47 d1k47b1 B:21-29,127-143,148-157,158-165,188-194
1oj4 d1oj4a1 A:24-37,127-139,139-148,150-155,159-163
1oj4 d1oj4b1 B:24-37,127-140,139-148,150-155,159-163
1fwk d1fwkc1 C:24-28,118-135,138-148,149-156,159-165
1fwl d1fwla1 A:24-28,118-135,138-148,149-156,159-165
1h74 d1h74c1 C:24-28,118-135,138-148,149-156,159-165
1h74 d1h74a1 A:24-28,118-135,138-148,149-156,159-165
1fwk d1fwka1 A:24-28,118-135,138-148,149-156,159-165
1uek d1ueka1 A:22-34,114-123,123-132,134-139,142-147
1fwk d1fwkd1 D:24-28,118-135,138-148,149-156,159-165
1h74 d1h74b1 B:24-28,118-135,138-148,149-156,159-165
1fwl d1fwlb1 B:24-28,118-135,138-148,149-156,159-165
1h74 d1h74d1 D:24-28,118-135,138-148,149-156,159-165
1h72 d1h72c1 C:24-28,118-135,138-148,149-156,159-165
1fwl d1fwlc1 C:24-28,118-135,138-147,149-156,159-165
1h73 d1h73a1 A:24-28,118-132,138-148,149-156,159-165
1fwk d1fwkb1 B:24-28,118-135,138-148,149-156,159-165
1fwl d1fwld1 D:24-28,118-135,138-148,149-156,159-165
5. d.358.1 YdfO-like
YdfO-like duplication: two alpha(2)-beta(3) motifs are related by pseudo twofold symmetry; single antiparrallel beta-sheet, order:321456
2hh8 d2hh8a1 A:37-45,75-90,92-104,106-113,114-122
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 824 (enumeration index: query510) of S5
2z28 B:5-11,273-286,287-297,310-318,342-346
2z28 A:4-11,273-286,287-297,310-318,342-346
3t81 A:82-87,300-313,315-332,345-352,356-364
3t81 B:82-87,301-313,315-332,345-352,356-364
2a2d A:57-62,167-183,187-197,201-207,210-216
3qt7 A:31-37,127-140,139-148,149-156,161-167
3qt7 B:31-37,127-140,139-148,149-156,161-167
2v2q B:23-34,116-129,128-137,138-144,148-152
2v2q A:23-34,116-129,128-137,138-144,148-152
3gon A:23-29,127-143,148-157,158-165,188-194
2z00 A:45-49,328-345,347-364,376-388,408-417
3n1g B:46-50,100-119,155-170,172-178,181-186
2z24 B:5-11,273-286,287-297,310-318,342-346
2z24 A:4-11,273-286,287-297,310-318,342-346
2vr2 A:57-62,354-367,370-380,401-409,434-443
2hk2 A:31-37,127-140,139-148,149-156,161-167
2hk2 B:31-37,127-140,139-148,149-156,161-167
2wg4 A:46-50,100-119,155-170,172-177,181-186
3e74 D:49-54,337-354,356-366,386-394,419-428
3e74 B:49-53,337-354,356-366,386-394,419-428
3e74 A:49-53,337-354,356-366,386-394,419-428
3e74 C:49-53,337-354,356-366,386-394,419-428
2hke B:34-41,135-145,144-153,154-161,168-177
2hke A:34-41,135-145,144-153,154-161,168-177
2z25 B:5-11,273-286,287-297,310-318,342-346
2z25 A:4-11,273-286,287-297,310-318,342-346
3q13 A:229-240,253-263,264-276,312-322,325-335
2gse B:63-68,360-373,376-386,407-415,440-449
2gse A:63-67,360-373,376-386,407-415,440-449
2gse D:63-67,360-373,376-386,407-415,440-449
2gse C:63-67,357-373,376-386,407-415,440-449
2v34 A:23-34,116-129,128-137,138-144,148-152
2v34 B:23-34,116-129,128-137,138-144,148-152
3mjm B:5-11,273-286,287-297,310-318,342-346
3mjm A:4-11,273-286,287-297,310-318,342-346
2z2a B:5-11,273-286,287-297,310-318,342-346
2z2a A:4-11,273-286,287-297,310-318,342-346
3mpg B:49-53,329-342,345-354,374-381,408-416
3mpg A:48-53,329-342,345-354,374-382,407-416
3d6n A:51-55,326-341,344-361,374-381,406-415
2zak B:4-14,21-46,48-64,293-302,303-311
2zak A:4-14,21-46,48-64,293-302,303-311
3m1n A:45-49,99-118,154-169,171-177,180-185
3m1n B:45-49,99-118,154-169,171-177,180-185
3t8l B:82-87,301-313,315-332,345-352,356-364
3t8l A:82-87,300-313,315-332,345-352,356-364
3gri B:48-52,328-341,344-353,373-381,406-415
3gri A:48-52,328-341,344-353,374-381,406-415
3k85 A:28-35,135-152,156-166,167-175,177-185
3k85 B:28-35,135-152,156-166,167-175,177-185
2ogj E:64-71,303-315,317-334,347-358,372-383
2ogj D:67-71,303-315,317-334,347-358,372-383
2ogj B:64-71,303-315,317-334,347-358,372-383
2ogj A:64-71,303-315,317-334,347-358,372-383
2ogj C:67-71,303-315,317-334,347-356,373-383
2o5r A:101-105,108-123,129-138,150-158,181-189
3qt5 A:31-37,127-140,139-148,149-156,161-167
3qt5 B:31-37,127-140,139-148,149-156,161-167
2z26 B:5-11,273-286,287-297,310-316,342-346
2z26 A:4-11,273-286,287-297,310-318,342-346
3ljq A:5-11,11-28,30-46,276-282,283-289
3ljq C:305-311,311-323,330-346,576-582,583-589
2a8j A:41-52,54-79,81-97,375-384,389-396
2a8j B:41-52,54-79,81-97,375-384,389-396
2ww4 B:24-37,127-140,139-148,150-155,158-163
2ww4 A:24-37,127-140,139-148,150-155,158-163
3c17 A:4-16,21-46,48-64,293-302,303-311
3c17 B:4-16,21-46,48-64,293-302,303-311
3nqb B:82-87,300-313,315-332,345-352,356-364
3nqb A:82-87,300-313,315-332,345-352,356-364
3jze C:6-12,274-287,288-298,311-319,343-347
3jze B:6-12,274-287,288-298,311-319,343-347
3jze D:6-12,274-287,288-298,311-319,343-347
3jze A:5-12,274-287,288-298,311-319,343-347
3d34 B:41-52,65-75,76-92,121-131,134-144
3d34 A:41-52,65-75,76-92,121-131,134-144
2aj4 A:67-72,194-210,215-224,228-235,237-244
2aj4 B:66-72,194-210,215-224,228-235,237-244
2z29 B:5-11,273-286,287-297,310-318,342-346
2z29 A:5-11,273-286,287-297,310-318,342-346
2a8m B:41-52,54-79,81-97,375-384,389-396
2a8m A:41-51,54-79,81-97,375-384,389-396
2a8l B:41-52,54-79,81-97,375-384,389-396
2a8l A:41-52,54-79,81-97,375-384,389-396
3hm7 D:53-57,338-355,357-367,388-396,421-430
3hm7 C:53-57,341-355,357-367,388-396,421-430
3hm7 B:53-57,338-355,357-374,388-396,421-430
3hm7 A:53-57,338-355,357-374,388-396,421-430
3hm7 E:53-57,338-355,357-367,388-396,421-430
3hm7 F:53-57,338-355,357-367,388-396,421-430
3iv8 D:49-54,309-322,324-341,355-362,364-372
3iv8 A:49-54,309-322,324-341,355-362,364-372
3iv8 B:49-54,309-322,324-341,355-362,364-372
3iv8 C:48-54,309-322,324-341,355-362,364-372
2e25 A:5-11,273-286,287-297,310-318,342-346
3k17 B:30-36,142-159,163-172,173-181,203-210
3k17 A:30-36,142-159,163-172,173-181,203-210
3k17 C:30-36,142-159,163-172,173-181,203-210
3k17 D:30-36,142-159,163-172,173-181,203-210
3n1o A:50-54,104-123,159-174,176-181,185-190
3n1o C:50-54,104-123,159-174,176-181,185-190
3hul B:18-22,107-120,121-131,132-140,141-149
3hul A:18-22,107-120,121-130,132-140,141-149
2a2c A:57-62,167-183,187-197,201-207,210-216
2vm8 D:63-67,360-373,376-386,407-415,440-449
2vm8 A:63-67,360-373,376-386,407-415,440-449
2vm8 C:63-67,360-373,376-386,407-415,440-449
2vm8 B:63-67,360-373,376-386,407-415,440-449
1ybq B:58-63,306-322,329-341,354-361,363-371
1ybq A:58-62,306-322,329-341,354-361,363-371
3k7g B:50-54,104-123,159-174,176-182,184-190
3f0n B:36-43,147-157,156-165,166-173,180-189
3f0n A:36-43,147-157,156-165,166-173,180-189
3dc8 A:46-50,338-354,357-367,389-396,421-430
3dc8 B:46-51,338-354,357-367,389-396,421-430
2a8i B:41-52,54-79,81-97,375-384,389-396
2a8i A:41-52,54-79,81-97,375-384,389-396
3lto A:38-43,143-156,155-164,165-171,172-177
3lto B:38-45,143-156,155-164,165-171,172-177
3d36 A:192-197,310-330,379-393,394-401,402-413
2gwn A:53-58,334-350,353-370,384-391,416-425
3pnu A:-1-5,260-273,274-284,298-304,330-334
2hk3 A:31-37,127-140,139-148,149-156,161-167
2hk3 B:31-37,127-140,139-148,149-156,161-167
2vun B:56-62,285-300,302-319,331-338,357-365
2vun D:56-62,285-300,302-319,331-338,357-365
2vun A:56-62,285-300,302-319,331-338,357-365
2vun C:56-62,285-300,302-319,331-338,357-365
2vf3 B:23-35,116-129,128-137,138-144,148-152
2vf3 A:23-35,116-129,128-137,138-144,148-152
2v8p B:23-35,116-129,128-137,138-144,148-152
2v8p A:23-34,116-129,128-137,138-144,148-152
2aqo B:58-62,306-322,329-341,354-361,363-371
3k7i B:50-54,104-123,159-174,176-182,184-190
3qt8 A:31-37,127-140,139-148,149-156,161-167
3qt8 B:31-37,127-140,139-148,149-156,161-167
3lm0 A:114-118,117-124,131-153,163-168,172-178
2v2v B:23-34,116-129,128-137,138-144,148-152
2v2v A:23-35,116-129,128-137,138-144,147-152
3qt6 A:31-37,127-140,139-148,149-156,161-167
3qt6 B:31-37,127-140,139-148,149-156,161-167
2vhl A:52-58,320-333,335-345,367-373,375-383
2vhl B:52-58,320-333,335-345,366-373,375-383
2z27 B:5-11,273-286,287-297,310-318,342-346
2z27 A:4-11,273-286,287-297,310-318,342-346
2v2z A:23-35,116-129,128-137,138-144,148-152
2v2z B:23-35,116-129,128-137,138-144,148-152
2aqv A:58-62,306-322,329-341,354-361,363-371
2aqv B:58-62,306-322,329-341,354-361,363-371
3egj B:48-54,309-322,324-341,355-362,364-372
3egj A:49-54,309-322,324-341,355-362,364-372
2gs8 A:31-38,127-140,139-148,149-156,157-163