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
1mb9 d1mb9a2 A:9-18,129-136,143-149,150-156,190-198
1llw d1llwa3 A:1-9,338-345,352-358,360-366,388-394
1llz d1llza3 A:1-9,338-345,352-358,360-366,388-394
1mbz d1mbzb2 B:9-18,129-137,143-149,150-156,189-198
1mc1 d1mc1b2 B:9-18,129-137,143-149,150-156,189-198
1m1z d1m1zb2 B:9-18,129-137,143-149,150-156,189-198
2vdc d2vdca3 A:1-9,339-346,353-359,361-367,387-396
2vdc d2vdcc3 C:1-9,339-346,353-359,361-367,387-396
1ea0 d1ea0a3 A:1-9,339-346,353-359,361-367,387-396
2vdc d2vdce3 E:1-9,339-346,353-359,361-367,387-396
1m1z d1m1za2 A:9-18,129-137,143-149,150-156,189-198
1mbz d1mbza2 A:9-18,129-137,143-149,150-156,189-198
1jgt d1jgtb2 B:9-18,129-137,143-149,150-156,189-198
1mb9 d1mb9b2 B:9-18,129-137,143-149,150-156,189-198
2vdc d2vdcd3 D:1-9,339-349,353-359,361-367,386-396
1ea0 d1ea0b3 B:1-9,339-349,353-359,361-367,386-396
2vdc d2vdcb3 B:1-9,339-349,353-359,361-367,386-396
2vdc d2vdcf3 F:1-9,339-349,353-359,361-367,386-396
1gph d1gph42 4:1-8,166-173,180-186,187-193,212-219
1ao0 d1ao0b2 B:1-8,166-173,180-186,187-193,212-219
1ao0 d1ao0c2 C:1-8,166-173,180-186,187-193,212-219
1ao0 d1ao0a2 A:1-8,166-173,180-186,187-193,212-219
1ao0 d1ao0d2 D:1-8,166-173,180-186,187-193,212-219
1jxa d1jxab2 B:1-8,168-175,178-184,185-191,209-216
1lm1 d1lm1a3 A:1-9,338-346,352-358,360-366,386-394
1gph d1gph32 3:1-8,166-176,180-186,187-193,211-219
1gph d1gph12 1:1-8,166-176,180-186,187-193,211-219
1gph d1gph22 2:1-8,166-176,180-186,187-193,211-219
1q15 d1q15c2 C:4-10,113-120,127-132,134-139,182-192
1jxa d1jxac2 C:1-8,168-175,178-184,185-191,208-216
1jgt d1jgta2 A:9-17,129-137,143-149,150-156,189-198
1q19 d1q19b2 B:4-10,113-120,127-132,134-139,182-192
1mc1 d1mc1a2 A:9-17,129-137,143-149,150-156,189-198
1q19 d1q19d2 D:4-10,113-120,127-132,134-139,182-192
1q19 d1q19a2 A:4-10,113-120,127-132,134-139,182-192
2bpl d2bplc2 C:1-8,168-175,178-184,185-191,209-216
1ecj d1ecjd2 D:1-8,176-183,190-197,201-208,227-234
2j6h d2j6ha2 A:1-8,168-175,178-184,185-191,209-216
2bpl d2bpla2 A:1-8,168-175,178-184,185-191,209-216
1jxa d1jxaa2 A:1-8,168-175,178-184,185-191,209-216
2bpl d2bplb2 B:1-8,168-175,178-184,185-191,209-216
1xfg d1xfgb_ B:1-8,168-175,178-184,185-191,209-216
1xff d1xffb_ B:1-8,168-175,178-184,185-191,209-216
1ecc d1ecca2 A:1-8,176-183,190-198,200-208,227-234
1xfg d1xfga_ A:1-8,168-175,178-184,185-191,209-216
1ecc d1eccb2 B:1-8,176-183,189-198,200-209,227-234
1xff d1xffa_ A:1-8,168-175,178-184,185-191,209-216
2j6h d2j6hb2 B:1-8,168-175,178-184,185-191,209-216
1ecb d1ecba2 A:1-8,176-183,190-198,200-208,227-234
1ofd d1ofdb3 B:1-9,338-347,352-358,360-366,386-395
1ofd d1ofda3 A:1-9,338-347,352-358,360-366,386-395
1ecj d1ecjb2 B:1-8,176-183,190-198,200-208,227-234
1ecb d1ecbc2 C:1-8,176-183,190-198,200-208,227-234
1ofe d1ofea3 A:1-9,338-347,352-358,360-366,386-395
1ecj d1ecjc2 C:1-8,176-183,190-198,200-208,227-234
1ofe d1ofeb3 B:1-9,338-347,352-358,360-366,386-395
1ecf d1ecfb2 B:1-8,176-184,190-198,200-208,226-234
1q15 d1q15b2 B:4-10,113-121,127-132,134-139,182-192
1q19 d1q19c2 C:4-10,113-121,127-132,134-139,182-192
1ecb d1ecbb2 B:1-8,176-183,190-198,200-208,227-234
1q15 d1q15a2 A:4-10,113-121,127-132,134-139,182-192
1ecj d1ecja2 A:1-8,176-183,190-198,200-208,226-234
1q15 d1q15d2 D:4-10,113-121,127-132,134-139,182-192
1ecf d1ecfa2 A:1-8,176-184,190-198,200-208,226-234
1ecg d1ecgb2 B:1-8,177-184,190-198,200-208,226-234
1ecg d1ecga2 A:1-8,176-184,190-198,200-208,226-234
1ecb d1ecbd2 D:1-8,176-184,190-198,200-208,226-234
2i3o d2i3ob1 B:59-68,245-251,331-339,341-350,396-402
2i3o d2i3od1 D:59-68,245-251,331-339,341-350,396-402
2e0w d2e0wb1 B:95-104,284-290,391-399,401-410,466-472
2i3o d2i3oa1 A:59-68,245-251,331-339,341-350,396-402
2e0w d2e0wa1 A:95-104,284-290,391-399,401-410,466-472
2i3o d2i3oc1 C:59-68,245-251,331-339,341-350,396-402
2nlz d2nlzd1 D:70-79,261-267,358-366,368-377,423-429
2nlz d2nlzb1 B:70-79,261-267,358-366,368-377,423-429
2nlz d2nlzc1 C:70-79,261-267,358-366,368-377,423-429
2nlz d2nlza1 A:70-79,261-267,358-366,368-377,423-429
1ct9 d1ct9a2 A:1-8,130-138,145-151,153-159,177-182
1ct9 d1ct9c2 C:1-8,130-139,145-151,153-159,176-182
1ct9 d1ct9d2 D:1-8,130-138,145-151,153-159,177-182
1ct9 d1ct9b2 B:1-8,130-140,145-151,153-159,176-182
2. d.194.1 CNF1/YfiH-like putative cysteine hydrolases
CNF1/YfiH-like putative cysteine hydrolases 4 layers: alpha/beta/beta/alpha; mixed beta sheets
2f9z d2f9zc1 C:8-15,16-25,26-36,37-46,129-137
1t8h d1t8ha_ A:107-112,116-123,125-134,135-144,262-269
1rv9 d1rv9a_ A:100-105,109-116,118-126,130-137,247-255
1xfj d1xfja_ A:96-101,105-112,114-123,124-133,252-260
1xaf d1xafa_ A:89-94,99-105,107-115,119-126,235-243
1xaf d1xafb_ B:89-94,99-105,107-115,119-126,235-243
1u05 d1u05b_ B:89-94,99-105,107-115,119-126,235-243
1rw0 d1rw0a_ A:89-94,99-105,107-115,119-126,235-243
1u05 d1u05a_ A:89-94,99-105,107-115,119-126,235-243
1rw0 d1rw0b_ B:89-94,99-105,107-115,119-126,235-243
2f9z d2f9zd1 D:9-15,17-25,26-36,37-47,129-137
1hzg d1hzga_ A:837-847,854-864,866-874,875-885,970-983
1hq0 d1hq0a_ A:837-847,854-864,866-874,875-885,970-983
3. b.1.18 E set domains "Early" Ig-like fold families possibly related to the immunoglobulin and/or fibronectin type III superfamilies !
Immunoglobulin-like beta-sandwich sandwich; 7 strands in 2 sheets; greek-key ! some members of the fold have additional strands
1wlh d1wlha3 A:756-768,781-789,792-800,803-812,849-857
1qfh d1qfha2 A:755-767,781-789,790-800,803-813,848-857
1qfh d1qfhb2 B:759-768,781-789,791-801,803-813,848-857
1wlh d1wlhb3 B:755-767,781-789,792-801,803-814,848-857
4. b.40.5 Inorganic pyrophosphatase
OB-fold barrel, closed or partly opened n=5, S=10 or S=8; greek-key
2ik4 d2ik4b1 B:15-22,40-52,56-61,66-71,88-96
1m38 d1m38b_ B:15-22,40-52,56-61,66-71,88-96
117e d117ea_ A:15-22,40-52,56-61,66-71,88-96
1wgj d1wgja_ A:15-22,40-52,56-61,66-71,88-96
1huk d1hukb_ B:15-22,40-51,56-61,66-71,91-96
1huj d1hujb_ B:15-22,40-51,56-61,66-71,91-96
1e6a d1e6aa_ A:15-22,40-51,56-61,66-71,91-96
1wgi d1wgia_ A:15-22,40-52,56-61,66-71,88-96
1m38 d1m38a_ A:15-22,40-51,56-61,66-71,91-96
2ihp d2ihpa1 A:15-22,40-51,56-61,66-71,91-96
1e9g d1e9ga_ A:15-22,40-51,56-61,66-71,91-96
1e9g d1e9gb_ B:15-22,40-51,56-61,66-71,91-96
1e6a d1e6ab_ B:1015-1022,1040-1051,1056-1061,1066-1071,1091-1096
2ik4 d2ik4a1 A:15-22,40-51,56-61,66-71,91-96
1wgi d1wgib_ B:15-22,40-51,56-61,66-71,91-96
1ypp d1yppb_ B:15-22,40-51,56-61,66-71,91-96
1huj d1huja_ A:15-22,40-51,56-61,66-71,91-96
2ihp d2ihpb1 B:15-22,40-51,56-61,66-71,91-96
1wgj d1wgjb_ B:15-22,40-51,56-61,66-71,91-96
1huk d1huka_ A:15-22,40-51,56-61,66-71,91-96
1ypp d1yppa_ A:15-22,40-51,56-61,66-71,91-96
8prk d8prkb_ B:1015-1022,1040-1050,1056-1061,1066-1071,1091-1096
8prk d8prka_ A:15-22,40-50,56-61,66-71,91-96
117e d117eb_ B:1015-1022,1040-1050,1056-1061,1066-1071,1091-1096
5. b.110.1 Cloacin translocation domain
Cloacin translocation domain complex fold made of several coiled beta-sheets
2b5u d2b5ua2 A:130-140,153-161,183-191,192-202,282-290
2b5u d2b5uc2 C:130-140,153-161,183-191,192-202,282-290
1jch d1jcha2 A:136-140,147-156,176-185,186-191,282-290
1jch d1jchc2 C:136-140,147-156,176-185,186-191,282-290
1rh1 d1rh1a1 A:119-129,138-147,169-177,178-188,279-287
1jch d1jchc2 C:136-140,147-156,176-185,190-197,282-290
1jch d1jcha2 A:136-140,147-156,176-185,190-197,282-290
6. c.66.1 S-adenosyl-L-methionine-dependent methyltransferases
S-adenosyl-L-methionine-dependent methyltransferases core: 3 layers, a/b/a; mixed beta-sheet of 7 strands, order 3214576; strand 7 is antiparallel to the rest
1vp3 d1vp3a_ A:169-177,187-192,193-197,207-214,220-225
3mag d3maga_ A:169-177,187-192,193-197,207-214,220-225
1jte d1jtea_ A:169-177,187-192,193-197,207-214,220-225
1eam d1eama_ A:169-177,187-192,193-197,207-214,220-225
3mct d3mcta_ A:169-177,187-192,193-197,207-214,220-225
1v39 d1v39a_ A:169-177,187-192,193-197,207-214,220-225
1jsz d1jsza_ A:169-177,187-192,193-197,207-214,220-225
2vp3 d2vp3a_ A:169-177,187-192,193-197,207-214,220-225
1b42 d1b42a_ A:169-177,187-192,193-197,207-214,220-225
1p39 d1p39a_ A:169-177,187-192,193-197,207-214,220-225
1vpt d1vpta_ A:169-177,187-192,193-197,207-214,220-225
1vp9 d1vp9a_ A:169-177,187-192,193-197,207-214,220-225
1jtf d1jtfa_ A:169-177,187-192,193-197,207-214,220-225
1eqa d1eqaa_ A:169-177,187-192,193-197,207-214,220-225
7. b.121.5 ssDNA viruses
Nucleoplasmin-like/VP (viral coat and capsid proteins) sandwich; 8 strands in 2 sheets; jelly-roll; some members can have additional 1-2 strands ! characteristic interaction between the domains of this fold allows the formation of five-fold and pseudo six-fold assemblies
1dnv d1dnva_ A:66-72,132-138,145-154,215-221,351-357
8. b.50.1 Acid proteases
Acid proteases barrel, closed; n=6, S=10, complex topology
1fmu d1fmua_ A:1-6,24-34,149-155,166-171,212-219
1czi d1czie_ E:1-6,24-34,149-155,163-168,209-217
1flh d1flha_ A:1-6,24-34,149-156,162-168,209-217
1yx9 d1yx9a1 A:1-6,24-34,149-156,162-168,209-217
3cms d3cmsa_ A:1-6,24-34,149-156,162-168,209-217
5pep d5pepa_ A:1-6,24-34,149-156,162-168,209-217
1psn d1psna_ A:1-6,24-34,149-156,162-168,208-217
1psa d1psab_ B:1-6,24-34,149-156,162-168,208-217
4cms d4cmsa_ A:1-6,24-34,149-156,162-168,208-217
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 305 (enumeration index: query2339) of S5
3tua A:70-76,82-89,93-100,102-109,170-179
3tu8 A:70-76,82-89,93-100,102-109,170-180
2axc A:125-135,148-156,178-186,187-197,277-284
2ik0 B:15-22,40-51,56-61,66-71,91-96
2ik0 A:15-22,40-52,56-61,66-71,88-96
3erc A:170-177,187-192,193-197,207-214,217-225
3erc B:170-177,187-192,193-197,207-214,217-225
3ohg A:73-85,124-131,217-225,229-238,306-313
3ooj F:1-8,168-175,178-184,185-191,209-216
3ooj D:1-8,168-175,178-184,185-191,209-216
3ooj C:1-8,168-173,178-184,185-191,210-216
3ooj A:1-8,168-175,178-184,185-191,210-216
3ooj E:1-8,168-175,178-184,185-191,209-216
3ooj B:1-8,168-175,178-184,185-191,209-216
3ooj H:1-8,168-175,178-184,185-191,209-216
3ooj G:1-8,168-175,178-184,185-191,209-216
2gn6 B:226-233,264-270,275-280,281-287,313-318
2gn6 A:226-233,264-269,275-280,281-287,314-318
3mdn D:3-9,193-202,209-216,217-224,240-247
3mdn A:3-9,193-202,209-216,217-224,240-247
3mdn C:3-9,193-202,208-216,217-225,240-247
3mdn B:3-9,193-202,208-216,217-225,240-247
2gn4 B:226-233,264-270,275-280,281-287,313-318
2gn4 A:226-233,264-269,275-280,281-287,314-318
2ik1 A:15-22,40-51,56-61,66-71,91-96
2ik1 B:15-22,40-52,56-61,66-71,88-96
2ik6 A:15-22,40-51,56-61,66-71,91-96
2ik6 B:15-22,40-52,56-61,66-71,88-96
3dr2 A:4-10,37-43,67-74,76-84,297-304
3dr2 B:5-10,37-43,67-74,76-84,297-304
2ik9 B:15-22,40-51,56-61,66-71,91-96
2ik9 A:15-22,40-52,56-61,66-71,88-96
2ik2 B:15-22,40-51,56-61,66-71,91-96
2ik2 A:15-22,40-50,56-61,66-71,91-96
2ik7 B:15-22,40-51,56-61,66-71,91-96
2ik7 A:15-22,40-51,56-61,66-71,91-96
2gn9 B:226-233,265-270,275-280,281-287,313-317
2gn9 A:226-233,265-270,275-280,281-286,313-317
3er8 A:170-177,187-192,193-197,207-214,217-225
3er8 B:170-177,187-192,193-197,207-214,217-225
2gna A:226-233,265-270,275-280,281-287,313-317
2gna B:226-233,265-270,275-280,281-287,313-317
1z9t A:89-94,99-105,107-115,119-126,235-242