1. d.58.28 Peptide methionine sulfoxide reductase common fold is elaborated with additional secondary structures !
Ferredoxin-like alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
1fva d1fvab_ B:63-71,72-83,127-140,156-161,163-185
1fvg d1fvga_ A:63-71,72-83,127-140,156-161,163-185
1fva d1fvaa_ A:63-71,72-83,127-140,156-161,163-185
1nwa d1nwaa_ A:4-12,13-24,64-77,93-99,100-118
1ff3 d1ff3b_ B:42-50,51-63,106-119,135-141,142-164
1ff3 d1ff3a_ A:42-50,51-63,106-119,135-141,142-164
1ff3 d1ff3c_ C:42-50,51-63,106-119,135-141,142-164
2gt3 d2gt3a1 A:42-50,51-63,106-119,135-140,142-164
2. d.185.1 LuxS/MPP-like metallohydrolase Share the same "active site motif" HxxEH located in the first core helix, but differ in one of the zinc-binding residues !
LuxS/MPP-like metallohydrolase core: beta-alpha-beta(2)-alpha(2); 2 layers: alpha/beta
1q2l d1q2la4 A:65-76,105-115,134-152,230-238,240-256
1q2l d1q2la4 A:65-76,85-97,134-152,230-238,240-256
2fge d2fgeb2 B:811-820,828-852,876-887,967-974,974-986
3. 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
2nqg d2nqga1 A:105-111,114-128,127-136,176-181,185-200
1kxr d1kxra_ A:105-111,114-128,127-136,176-181,185-200
2g8e d2g8ea1 A:105-110,114-128,127-136,177-181,185-200
1kfu d1kful3 L:96-101,104-118,117-126,166-171,175-190
1kxr d1kxrb_ B:106-110,114-128,127-136,177-181,185-200
2ary d2arya1 A:106-111,114-128,127-136,176-181,185-200
1mdw d1mdwa_ A:96-100,104-118,117-126,167-171,175-190
1df0 d1df0a3 A:96-101,104-118,117-126,166-171,175-190
1kfx d1kfxl3 L:96-101,104-118,117-126,166-171,175-190
1zcm d1zcma1 A:106-111,114-128,127-136,176-181,185-200
1tl9 d1tl9a_ A:105-110,114-128,127-136,177-181,185-200
1u5i d1u5ia3 A:96-101,104-118,117-126,166-171,175-190
1qxp d1qxpa4 A:96-101,104-118,117-126,166-171,176-190
4. d.58.34 Formiminotransferase domain of formiminotransferase-cyclodeaminase. duplication: contains two subdomains of this fold !
Ferredoxin-like alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
1qd1 d1qd1b1 B:2003-2013,2016-2031,2054-2074,2087-2098,2100-2120
1qd1 d1qd1a1 A:3-13,16-31,54-74,87-98,100-120
1qd1 d1qd1a2 A:182-190,192-204,245-261,263-270,295-308
1qd1 d1qd1b2 B:2182-2190,2192-2204,2245-2261,2263-2270,2295-2308
5. 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
1g65 d1g65t_ T:44-54,168-181,185-206,207-217,225-241
1g0u d1g0ut_ T:44-54,168-180D,185-206,207-217,225-241
1g65 d1g65f_ F:44-54,168-180D,185-206,207-217,225-241
1ryp d1rypg_ G:43-53,167-183,187-207,210-220,231-247
1ryp d1rypu_ U:43-53,167-183,187-207,210-220,231-247
1g0u d1g0uf_ F:44-54,168-180D,185-206,207-217,225-241
1j2q d1j2qj_ J:10-19,128-137,147-167,170-180,187-197
1yar d1yarl1 L:10-19,128-142,147-167,170-179,188-200
1yau d1yauk1 K:10-19,128-142,147-167,170-179,188-200
1yar d1yarj1 J:10-19,128-142,147-167,170-179,188-200
1yar d1yark1 K:10-19,128-142,147-167,170-179,188-200
1ya7 d1ya7l1 L:10-19,128-142,147-167,170-179,188-200
1yar d1yari1 I:10-19,128-142,147-167,170-179,188-200
1yar d1yarm1 M:10-19,128-142,147-167,170-179,188-200
1yau d1yauj1 J:10-19,128-142,147-167,170-179,188-200
1ya7 d1ya7m1 M:10-19,128-142,147-167,170-179,188-200
1iru d1iruu_ U:43-53,168-180,185-202,208-218,228-245
1yau d1yaul1 L:10-19,128-142,147-167,170-179,188-200
1iru d1irug_ G:43-53,168-180,185-202,208-218,228-245
1yar d1yarh1 H:10-19,128-142,147-167,170-179,188-200
1ya7 d1ya7k1 K:10-19,128-142,147-167,170-179,188-200
1yau d1yaui1 I:10-19,128-142,147-167,170-179,188-200
1yar d1yarn1 N:10-19,128-142,147-167,170-179,188-200
1j2q d1j2ql_ L:10-19,128-136,147-167,170-180,187-197
1yau d1yaum1 M:10-19,128-142,147-167,170-179,188-200
1j2q d1j2qh_ H:10-19,128-136,147-167,170-180,187-197
1j2q d1j2qn_ N:10-19,128-136,147-167,170-180,187-197
1ya7 d1ya7i1 I:10-19,128-142,147-167,170-179,188-200
1j2q d1j2qm_ M:10-19,128-136,147-167,170-180,187-197
1j2q d1j2qi_ I:10-19,128-136,147-167,170-180,187-197
1j2q d1j2qk_ K:10-19,128-136,147-167,170-180,187-197
1yau d1yaun1 N:10-19,128-142,147-167,170-179,188-200
1jd2 d1jd21_ 1:44-54,168-180D,185-206,207-217,225-241
1jd2 d1jd2f_ F:44-54,168-180D,185-206,207-217,225-241
2gpl d2gpls1 S:44-52,168-180,185-201,2E-217,225-233
2gpl d2gple1 E:44-52,168-180,185-201,2E-217,225-233
2h6j d2h6jk1 K:10-17,140-151,159-179,192-199,206-219
2h6j d2h6jl1 L:10-17,140-151,159-179,192-199,206-219
2h6j d2h6jn1 N:10-17,140-151,159-179,192-199,206-219
2h6j d2h6ji1 I:10-17,140-151,159-179,192-199,206-219
2h6j d2h6jj1 J:10-17,140-151,159-179,192-199,206-219
2h6j d2h6jm1 M:10-17,140-151,159-179,192-199,206-219
1g0u d1g0uc_ C:44-52,168-180A,185-202,209-217,225-243
2h6j d2h6jh1 H:10-17,140-151,159-179,192-199,206-219
1q5q d1q5qh_ H:10-17,140-151,159-179,192-199,206-224
1q5q d1q5qi_ I:10-17,140-151,159-179,192-199,206-224
1q5q d1q5qj_ J:10-17,140-151,159-179,192-199,206-224
1q5q d1q5qm_ M:10-17,140-151,159-179,192-199,206-224
1q5q d1q5qk_ K:10-17,140-151,159-179,192-199,206-224
1q5q d1q5qn_ N:10-17,140-151,159-179,192-199,206-224
1q5q d1q5ql_ L:10-17,140-151,159-179,192-199,206-224
6. c.1.11 Enolase C-terminal domain-like binds metal ion (magnesium or manganese) in conserved site inside barrel ! N-terminal alpha+beta domain is common to this superfamily !
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
2ptw d2ptwa1 A:162-172,175-199,217-233,237-244,275-286
1oep d1oepa1 A:163-172,175-199,217-233,237-244,270-286
2ptz d2ptza1 A:163-172,175-199,217-233,237-244,270-286
2pu1 d2pu1a1 A:163-172,175-199,217-233,237-244,270-286
2al2 d2al2a1 A:166-175,178-202,220-236,240-247,274-290
1p43 d1p43b1 B:665-675,678-702,720-736,740-747,774-790
1l8p d1l8pd1 D:1667-1675,1678-1702,1720-1736,1740-1747,1774-1790
2al1 d2al1b1 B:166-175,178-202,220-236,240-247,274-290
3enl d3enla1 A:167-175,178-202,220-236,240-247,274-290
2al2 d2al2b1 B:167-175,178-202,220-236,240-247,274-290
1els d1elsa1 A:167-175,178-202,220-236,240-247,274-290
7. d.58.33 Formylmethanofuran:tetrahydromethanopterin formyltransferase duplication: contains two subdomains of this fold !
Ferredoxin-like alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2
2fhj d2fhjc1 C:12-28,29-42,81-101,102-108,119-129
2fhk d2fhkd1 D:12-28,29-42,81-101,102-108,119-129
2fhk d2fhkb1 B:12-28,29-42,81-101,102-108,119-129
2fhk d2fhka1 A:12-28,29-42,81-101,102-108,119-129
2fhk d2fhkc1 C:12-28,29-42,81-101,102-108,119-129
1m5s d1m5sc1 C:2011-2028,2029-2042,2080-2100,2101-2106,2116-2126
2fhj d2fhjb1 B:11-28,29-42,81-101,102-108,119-129
1ftr d1ftra1 A:11-28,29-42,81-101,102-108,119-129
1ftr d1ftrb1 B:11-28,29-42,81-101,102-108,119-129
1ftr d1ftrc1 C:11-28,29-42,81-101,102-108,119-129
2fhj d2fhjd1 D:12-28,29-42,81-100,102-108,119-129
1ftr d1ftrd1 D:12-28,29-42,81-100,102-108,119-129
1m5s d1m5sa1 A:11-28,29-42,80-99,101-106,116-126
1m5s d1m5sb1 B:1011-1028,1029-1042,1080-1099,1101-1106,1116-1126
2fhj d2fhja1 A:11-28,29-42,81-100,102-108,119-129
1m5s d1m5sd1 D:3011-3028,3029-3042,3080-3099,3101-3106,3116-3126
1m5h d1m5hf1 F:5011-5028,5029-5042,5080-5099,5101-5107,5116-5126
1m5h d1m5hd1 D:3010-3028,3029-3042,3080-3099,3101-3106,3116-3126
8. d.280.1 Sulfolobus fructose-1,6-bisphosphatase-like
Sulfolobus fructose-1,6-bisphosphatase-like 4 layers: a/b/b/a; antiparallel beta sheets; similarities to ferredoxin-like fold (scop_cf 54861) in the N-terminal part (1-120) and to the Bacterial S-adenosylmethionine decarboxylase subunit (scop_fa 997656) in the C-terminal part (121-340)
1umg d1umga_ A:124-133,135-149,247-258,290-301,313-334
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 847 (enumeration index: query1166) of S5
3e4a A:84-96,105-117,157-172,253-261,263-279
3e4a A:84-96,125-135,157-172,253-261,263-279
3eoq A:23-34,43-55,91-108,182-190,192-207
3eoq B:23-34,43-55,91-108,182-190,192-207
2iem A:42-50,51-63,106-118,135-140,142-164
3n56 B:84-96,105-117,157-172,253-261,263-279
2g54 A:84-96,125-135,157-172,253-261,263-278
2waq C:120-125,133-146,257-264,271-275,276-285
3otr B:172-181,184-208,226-242,246-253,282-298
2g56 B:84-96,123-135,157-172,253-261,263-279
2g56 A:84-96,123-135,157-172,253-261,263-279
3f2b A:618-626,627-646,653-662,663-669,687-695
3amj C:53-65,74-86,125-140,215-223,225-241
3jtl I:10-19,128-142,147-167,170-179,188-200
3jtl K:10-19,128-142,147-167,170-179,188-200
3e0m D:0-9,10-21,63-75,92-98,99-118
3e0m C:0-8,10-21,63-75,93-97,99-118
3e0m B:2-9,10-21,63-75,92-98,99-118
3e0m A:1-8,10-21,63-75,93-97,99-118
2fhg P:310-317,439-458,459-478,492-499,506-522
2fhg R:310-317,439-458,459-478,492-499,506-522
3df0 A:96-101,104-118,117-126,166-171,175-190
3ofi A:84-96,105-117,157-172,253-261,263-279
3ofi B:84-96,105-117,157-172,253-261,263-278
3t2d A:124-133,135-149,247-258,300-311,323-344
3okj C:44-52,168-18A,185-202,209-217,225-243
3okj S:44-52,168-180,185-201,2E-217,225-233
3okj E:44-52,168-180,185-201,2E-217,225-233
3okj Q:44-52,168-18A,185-202,209-217,225-243
3pil A:16-24,25-38,88-101,117-123,124-143
3pil B:16-24,25-38,88-101,117-123,124-143
2wk3 B:84-96,125-135,157-172,253-261,263-279
2wk3 B:84-96,105-117,157-172,253-261,263-279
2wk3 A:84-96,105-117,157-172,253-261,263-279
2wk3 A:84-96,125-135,157-172,253-261,263-279
3jrm K:10-19,128-142,147-167,170-179,188-200
3tuv A:84-96,125-135,157-172,253-261,263-278
3t2g A:124-133,135-149,247-258,300-311,323-344
3e0d B:92-101,102-121,128-137,138-144,158-174
3e0d A:92-101,102-121,128-137,138-144,158-174
2wby B:84-96,105-117,157-172,253-261,263-278
2wby A:84-96,125-135,157-172,253-261,263-279
2wby B:84-96,125-135,157-172,253-261,263-278
2wc0 A:84-96,105-117,157-172,253-261,263-279
2wc0 A:84-96,125-135,157-172,253-261,263-279
2wc0 B:84-96,105-117,157-172,253-261,263-279
3e4z B:84-96,105-117,157-172,253-261,263-278
2pfd A:181-191,192-205,245-261,262-270,295-308
2pfd C:181-191,192-205,245-261,262-270,295-308
2pfd B:181-191,192-205,245-261,262-270,295-308
2pfd C:3-13,16-31,54-73,87-98,100-120
2pfd D:181-191,192-205,245-261,262-270,295-308
2pfd B:3-13,16-31,54-73,87-98,100-120
2pfd A:3-13,16-31,54-73,87-98,100-120
2pfd D:3-13,16-31,54-73,87-98,100-120
3r1m A:124-133,135-149,247-258,290-301,313-334
2jg4 B:84-96,105-117,157-172,253-261,263-279
2jg4 A:84-96,123-135,157-172,253-261,263-279
2jbu B:84-96,125-135,157-172,253-261,263-279
3bqf A:197-206,207-219,262-275,291-297,298-317
3f2c A:618-626,627-646,653-662,663-669,687-695
3hkz M:120-125,133-146,257-264,271-275,276-285
3h44 B:84-96,105-117,157-172,253-261,263-278
3h44 A:84-96,105-117,157-172,253-261,263-278
3h44 A:84-96,125-135,157-172,253-261,263-278
3jse M:10-19,128-142,147-167,170-179,188-200
3jse N:10-19,128-142,147-167,170-179,188-200
3jse I:10-19,128-142,147-167,170-179,188-200
3jse L:10-19,128-142,147-167,170-179,188-200
3jse K:10-19,128-142,147-167,170-179,188-200
3jse J:10-19,128-142,147-167,170-179,188-200
3n57 B:84-96,105-117,157-172,253-261,263-278
3n57 A:84-96,105-117,157-172,253-261,263-279
3n57 A:84-96,125-135,157-172,253-261,263-279
3n57 B:84-96,125-135,157-172,253-261,263-278
3p7o A:84-96,125-135,157-172,253-261,263-278
3t2f A:124-133,135-149,247-258,300-311,323-344
3bqh A:197-205,207-219,262-274,292-297,298-317
3nzx C:44-52,168-18A,185-202,209-217,225-243
3nzx Q:44-52,168-18A,185-202,209-217,225-243
2g47 A:84-96,105-117,157-172,253-261,263-279
2g47 B:84-96,123-135,157-172,253-261,263-279
2g47 A:84-96,123-135,157-172,253-261,263-279
3t2e A:124-133,135-149,247-258,300-311,323-344
2j89 A:37-45,46-57,101-114,130-136,137-156
3mg4 S:44-52,168-180,185-201,209-217,225-233
3mg4 E:44-52,168-180,185-201,207E-217,225-233
3f2d A:618-626,627-646,653-662,663-670,687-695
3e50 B:84-96,105-117,157-172,253-261,263-279
3e50 A:84-96,105-117,157-172,253-261,263-279
3e50 B:84-96,123-135,157-172,253-261,263-279
3e50 A:84-96,125-135,157-172,253-261,263-279
2hnh A:81-89,90-108,117-125,127-133,147-163
2p0r B:88-92,96-110,109-118,159-163,167-182
3pin B:16-24,25-38,88-101,117-123,124-143
3t2c A:124-133,135-149,247-258,300-311,323-344
3cww B:84-96,105-117,157-172,253-261,263-279
3cww A:84-96,105-117,157-172,253-261,263-279
3e0f A:81-90,95-124,183-195,195-201,214-225
3p7l A:84-96,125-135,157-172,253-261,263-278
3pim C:16-24,25-38,88-101,117-122,124-143
3pim A:16-24,25-38,88-101,116-123,124-143
3pim B:16-24,25-38,88-101,117-123,124-143
2xh2 D:165-174,178-202,220-236,240-247,274-290
3mg6 E:44-52,168-180,185-201,207E-217,225-233
2hpi A:92-101,102-121,128-137,138-144,158-174
1tt9 A:181-191,192-205,245-261,262-270,295-308
1tt9 C:181-190,192-205,245-261,263-270,295-308
1tt9 B:181-190,192-205,245-261,263-270,295-308
1tt9 C:3-13,16-31,55-73,87-98,100-120
1tt9 D:181-191,192-205,245-261,262-270,295-308
1tt9 B:3-13,16-31,55-73,87-98,100-120
1tt9 A:3-13,16-31,55-73,87-98,100-120
1tt9 D:3-13,16-31,55-73,87-98,100-120
3bqe A:197-206,207-218,262-274,291-296,298-317
3hgz B:84-96,105-117,157-172,253-261,263-279
3hgz A:84-96,105-117,157-172,253-261,263-279
3hgz B:84-96,125-135,157-172,253-261,263-279
3pm9 F:349-357,361-378,411-427,428-433,438-448
3t2b A:124-133,135-149,247-258,300-311,323-344
2hqa A:81-89,90-108,117-125,127-133,147-163
2hpm A:92-101,102-121,128-137,138-144,158-174
3bqg A:197-206,207-219,262-274,291-296,298-317