1. d.2.1 Lysozyme-like
Lysozyme-like common alpha+beta motif for the active site region
2igs d2igsf1 F:144-150,168-179,185-199,200-216
2igs d2igse1 E:144-150,168-179,185-199,200-215
2igs d2igsh1 H:144-150,168-179,185-199,200-215
2igs d2igsd1 D:144-150,168-179,185-199,200-215
2igs d2igsc1 C:144-150,168-179,185-199,200-215
2igs d2igsb1 B:144-150,168-179,185-199,200-215
2igs d2igsg1 G:144-150,168-179,185-199,200-215
2igs d2igsa1 A:144-149,168-179,185-199,200-215
2. a.89.1 Methyl-coenzyme M reductase alpha and beta chain C-terminal domain
Methyl-coenzyme M reductase alpha and beta chain C-terminal domain multihelical bundle; contains buried central helix
1hbu d1hbub1 B:6-13,207-227,229-247,427-443
1hbu d1hbue1 E:6-13,207-227,229-247,427-443
1hbn d1hbne1 E:6-13,207-227,229-247,427-443
1hbm d1hbme1 E:6-13,207-227,229-247,427-443
1hbo d1hbob1 B:6-13,207-227,229-247,427-443
1hbn d1hbnb1 B:6-13,207-227,229-247,427-443
1hbm d1hbmb1 B:6-13,207-227,229-247,427-443
1mro d1mroe1 E:6-13,207-227,229-247,427-440
1mro d1mrob1 B:6-13,207-227,229-247,427-440
1hbo d1hboe1 E:6-13,207-227,229-247,427-440
1e6v d1e6vb1 B:7-14,208-228,231-248,428-442
1e6v d1e6ve1 E:7-14,208-228,231-248,428-442
1e6y d1e6yb1 B:2004-2010,2204-2224,2226-2244,2425-2432
1e6y d1e6ye1 E:5004-5010,5204-5224,5226-5244,5425-5432
1e6y d1e6yd1 D:4085-4089,4312-4339,4343-4352,4544-4555
1e6y d1e6ya1 A:1085-1089,1312-1339,1343-1352,1544-1555
1hbo d1hboa1 A:71-75,299-326,330-339,524-535
1hbu d1hbua1 A:71-75,299-326,330-339,524-535
1mro d1mrod1 D:71-75,299-326,330-339,524-535
1mro d1mroa1 A:71-75,299-326,330-339,524-535
1hbn d1hbna1 A:71-75,299-326,330-339,524-535
1hbu d1hbud1 D:71-75,299-326,330-339,524-535
1hbn d1hbnd1 D:71-75,299-326,330-339,524-535
1hbo d1hbod1 D:71-75,299-326,330-339,524-535
1hbm d1hbmd1 D:71-75,299-326,330-339,524-535
1e6v d1e6va1 A:74-78,302-329,333-342,527-538
1e6v d1e6vd1 D:74-78,302-329,333-342,527-538
1hbm d1hbma1 A:71-75,299-326,330-339,524-535
3. b.82.2 Clavaminate synthase-like Iron and ketoglutarate-dependent enzymes; elaborated version of this common fold !
Double-stranded beta-helix one turn of helix is made by two pairs of antiparallel strands linked with short turns ! has appearance of a sandwich of distinct architecture and jelly-roll topology
1e5r d1e5rb_ B:101-109,208-222,223-241,244-260
1e5s d1e5sb_ B:101-109,208-222,223-241,244-260
1e5s d1e5sa_ A:101-109,208-222,223-241,244-260
4. a.71.2 Helical domain of Sec23/24
ERP29 C domain-like 5 helices; bundle
1m2v d1m2vb1 B:139-144,667-691,704-720,912-926
1pd0 d1pd0a1 A:139-143,667-691,704-720,912-926
5. c.1.18 PLC-like phosphodiesterases
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
1qas d1qasa3 A:304-311,524-536,535-547,563-571
1qas d1qasb3 B:304-311,524-536,535-547,563-571
1qat d1qatb3 B:304-311,524-536,535-547,563-571
6. e.29.1 beta and beta-prime subunits of DNA dependent RNA-polymerase The catalytic site is formed by the association of two double-psi beta-barrel domains, one from each subunit !
beta and beta-prime subunits of DNA dependent RNA-polymerase Multidomain subunits of complex domain organization
2ppb d2ppbd1 D:1117-1122,1254-1265,1340-1360,1364-1377
2o5i d2o5id1 D:1117-1122,1255-1265,1340-1360,1364-1377
2o5i d2o5in1 N:1117-1122,1255-1265,1340-1360,1364-1377
2cw0 d2cw0d1 D:1117-1122,1254-1265,1340-1360,1364-1377
1zyr d1zyrd1 D:1117-1122,1254-1265,1340-1360,1364-1377
2be5 d2be5d1 D:1117-1122,1254-1265,1340-1360,1364-1377
2a68 d2a68d1 D:1117-1122,1254-1265,1340-1360,1364-1377
2be5 d2be5n1 N:1117-1122,1254-1265,1340-1360,1364-1377
1zyr d1zyrn1 N:1117-1122,1254-1265,1340-1360,1364-1377
2a6h d2a6hd1 D:1117-1122,1254-1265,1340-1360,1364-1377
2a6e d2a6ed1 D:1117-1122,1254-1265,1340-1360,1364-1377
2a6h d2a6hn1 N:1117-1122,1254-1265,1340-1360,1364-1377
2a69 d2a69d1 D:1117-1122,1254-1265,1340-1360,1364-1377
2a68 d2a68n1 N:1117-1122,1254-1265,1340-1360,1364-1377
1iw7 d1iw7d_ D:1117-1122,1254-1265,1340-1360,1364-1377
2a6e d2a6en1 N:1117-1122,1254-1265,1340-1360,1364-1377
2a69 d2a69n1 N:1117-1122,1254-1265,1340-1360,1364-1377
1iw7 d1iw7n_ N:1117-1122,1254-1265,1340-1360,1364-1377
3dxj d3dxjn1 N:1117-1122,1254-1265,1340-1360,1364-1377
1smy d1smyd_ D:1117-1122,1254-1265,1340-1360,1364-1377
2cw0 d2cw0n1 N:1117-1122,1254-1265,1340-1360,1364-1377
1smy d1smyn_ N:1117-1122,1254-1265,1340-1360,1364-1377
3dxj d3dxjd1 D:1117-1122,1254-1265,1340-1360,1364-1377
2ppb d2ppbn1 N:1117-1122,1254-1265,1340-1360,1364-1377
1i6v d1i6vd_ D:1117-1122,1254-1265,1340-1360,1364-1377
2o5j d2o5jd1 D:1117-1122,1245-1265,1340-1360,1364-1377
7. i.8.1 RNA polymerase
RNA polymerase
1l9z d1l9zd_ D:1117-1122,1257-1265,1339-1360,1364-1377
1l9u d1l9ud_ D:1117-1122,1257-1265,1340-1360,1364-1377
1l9u d1l9um_ M:1117-1122,1257-1265,1340-1360,1364-1377
1hqm d1hqmd_ D:1118-1123,1255-1266,1341-1361,1365-1378
8. 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
1i39 d1i39a_ A:16-24,26-34,42-58,132-158
1i3a d1i3aa_ A:16-24,26-34,42-58,132-158
1uax d1uaxb_ B:17-27,26-37,45-61,138-164
1uax d1uaxa_ A:17-27,26-37,45-61,138-164
1eke d1ekeb_ B:17-27,26-37,45-61,152-178
1eke d1ekea_ A:17-27,26-37,45-61,152-178
1io2 d1io2a_ A:17-27,26-37,45-60,138-164
2dfh d2dfha1 A:17-27,26-37,45-60,138-164
1x1p d1x1pa1 A:16-27,26-37,45-60,138-164
9. c.56.7 AF0625-like contains extra C-terminal alpha/beta domain: 3 layers, a/b/a; parallel beta-sheet of 4 strands, order 2134 !
Phosphorylase/hydrolase-like core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops
2gfq d2gfqb1 B:87-96,113-128,164-182,201-211
10. a.227.1 ERO1-like similar active site architecture to
ERO1-like multihelical; consists of 2 four-helical bundles
1rq1 d1rq1a_ A:81-87,192-208,329-351,352-379
1rp4 d1rp4a_ A:81-87,192-207,329-351,352-379
11. c.6.2 Glycoside hydrolase/deacetylase in the different families beta-barrels are similarly distorted but may vary in the number of strands !
7-stranded beta/alpha barrel variant of beta/alpha barrel; parallel beta-sheet barrel, closed, n=7, S=8; strand order 1234567; some members may have fewer strands
1ufa d1ufaa2 A:1-11,317-344,353-362,361-378
12. c.76.1 Alkaline phosphatase-like
Alkaline phosphatase-like core:3 layers: a/b/a; mixed beta-sheet of 8 strands, order 43516728, strand 7 is antiparallel to the rest
1ejj d1ejja2 A:4-13,375-390,399-408,410-436
1eqj d1eqja2 A:4-13,375-390,399-408,410-436
13. c.1.4 FMN-linked oxidoreductases
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
1gox d1goxa_ A:123-129,133-148,198-207,212-224
1al7 d1al7a_ A:123-129,133-148,198-207,212-224
14. i.16.1 GroE chaperon
GroE chaperon
1gru d1grun_ N:183-191,281-297,338-356,358-373
1gru d1gruj_ J:183-191,281-297,338-356,358-373
1gru d1gruh_ H:183-191,281-297,338-356,358-373
1gru d1grui_ I:183-191,281-297,338-356,358-373
15. d.248.1 Coproporphyrinogen III oxidase
Coproporphyrinogen III oxidase alpha-beta(6)-alpha(2)-beta-alpha(n); 3 layers alpha/beta/alpha; antiparallel sheet: order 1234567
3dwr d3dwrb1 B:122-134,138-157,195-224,285-298
1tkl d1tklb_ B:144-159,163-183,220-249,311-323
1tkl d1tkla_ A:144-159,163-183,220-249,311-323
3dws d3dwsa1 A:121-134,138-157,195-224,285-298
2qt8 d2qt8a1 A:121-134,138-157,195-224,285-298
1vju d1vjub_ B:129-142,146-165,203-232,293-306
2qt8 d2qt8b1 B:121-134,138-157,195-224,285-298
1vju d1vjua_ A:129-142,146-165,203-232,293-306
3dws d3dwsb1 B:121-134,138-157,195-224,285-298
3dwr d3dwra1 A:121-134,138-157,195-224,285-298
1tlb d1tlbw_ W:144-159,163-183,220-249,311-323
1tlb d1tlbq_ Q:144-159,163-183,220-249,311-323
1tlb d1tlbs_ S:144-159,163-183,220-249,311-323
1tlb d1tlbd_ D:144-159,163-183,220-249,311-323
1tlb d1tlba_ A:144-159,163-183,220-249,311-323
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 159 (enumeration index: query107) of S4
3rc8 A:257-261,604-613,621-646,651-673
3jzm C:39-47,121-138,146-154,156-175
3m2r E:6-13,207-227,229-247,427-440
3m2r A:71-75,299-326,330-339,524-535
3m2r D:71-75,299-326,330-339,524-535
3m2r B:6-13,207-227,229-247,427-443
3ez6 A:145-152,173-181,183-193,257-267
3ez6 B:145-152,173-181,183-193,257-267
2d0a A:107-117,116-127,142-151,235-261
3m2u D:71-75,299-326,330-339,524-535
3m2u A:71-75,299-326,330-339,524-535
3m2u E:6-13,207-227,229-247,427-443
3m2u B:6-13,207-227,229-247,427-443
3iuj A:14-22,537-552,566-574,589-600
3tal B:77-88,154-184,190-204,262-290
3tal A:77-88,154-184,190-205,262-290
3ez2 B:145-152,173-181,183-192,257-267
3ez2 A:145-152,173-181,183-193,257-267
3ahr A:76-80,192-208,367-392,394-418
3dry C:45-51,68-76,77-84,95-109
3sqg H:3-10,202-222,224-242,423-433
3sqg D:79-83,313-340,344-353,543-554
3sqg B:3-10,202-222,224-242,423-433
3sqg A:79-83,313-340,344-353,543-554
3sqg E:3-10,202-222,224-242,423-433
3sqg G:79-83,313-340,344-353,543-554
3m1c A:260-269,351-366,375-401,404-427
2dfe A:16-27,26-37,45-60,138-164
3aoi D:1117-1122,1254-1265,1340-1360,1364-1377
3aoi I:1117-1122,1254-1265,1340-1360,1364-1377
3aoi N:1117-1122,1254-1265,1340-1360,1364-1377
1v73 A:202-208,211-218,220-234,266-278
3p83 F:16-24,26-34,42-57,132-158
3p83 E:16-24,26-34,42-57,132-158
3p83 D:16-24,26-34,42-57,132-158
2aex A:272-285,289-308,346-375,437-449
2p0y A:162-169,179-189,198-210,209-219
3aoh N:1117-1122,1254-1265,1340-1360,1364-1377
3aoh I:1117-1122,1254-1265,1340-1360,1364-1377
3aoh D:1117-1122,1253-1265,1340-1360,1364-1377
3drx E:45-51,68-76,77-84,95-109
3iko E:207-213,466-485,486-497,499-515
3iko B:207-213,466-485,486-497,499-515
3iko H:207-213,466-485,486-497,499-515
3m30 A:71-75,299-326,330-339,524-535
3m30 E:6-13,207-227,229-247,427-443
3m30 B:6-13,207-227,229-247,427-443
3m30 D:71-75,299-326,330-339,524-535
2nli A:140-146,150-165,195-203,223-235
3kje A:30-37,62-71,81-91,113-132
2j6x E:140-146,150-165,195-202,223-235
2j6x A:140-146,150-165,195-202,223-235
2j6x B:140-146,150-165,195-203,223-235
3p0b A:1-11,317-344,353-362,361-378
3k0c A:39-47,118-138,146-154,156-175
3ihv B:73-77,418-435,469-486,488-499
3ihv A:73-77,418-435,469-486,488-499
3bg1 F:207-214,466-485,486-497,499-515
3bg1 B:207-214,466-485,486-497,499-515
3bg1 G:207-214,466-485,486-497,499-515
3bg1 C:207-214,466-485,486-497,499-515
2d0c A:107-117,116-127,135-151,235-261
3bg0 B:207-214,466-485,486-497,499-515
3bg0 C:207-214,466-485,486-497,499-515
3bg0 F:207-214,466-485,486-497,499-515
3bg0 G:207-214,466-485,486-497,499-515
3nav A:17-25,29-44,62-75,77-93
3hl6 B:67-72,99-111,151-166,170-186
3hl6 B:67-72,111-122,151-166,170-186
3hl6 B:51-58,111-122,151-166,170-186
3hl6 A:51-58,111-121,151-166,170-186
3hl6 A:67-73,111-121,151-166,170-186
3eql N:1117-1122,1254-1265,1340-1360,1364-1377
3eql D:1117-1122,1254-1265,1340-1360,1364-1377
2bkl A:8-16,532-547,561-569,583-594
2bkl B:8-16,532-547,561-569,583-594
2zfa A:140-146,150-165,195-203,223-235
3mun A:14-22,537-552,566-574,589-600
3nvj A:81-86,193-208,329-351,352-379
3eq7 A:15-20,553-568,582-589,604-615
3pot B:6-13,207-227,229-247,427-443
3pot D:71-75,299-326,330-339,524-535
3pot A:71-75,299-326,330-339,524-535
3pot E:6-13,207-227,229-247,427-443
3m31 A:81-87,192-207,329-351,352-379
3eh1 A:523-528,1034-1057,1068-1084,1254-1268
3ahq A:76-80,192-208,367-392,394-418
3m1v A:71-75,299-326,330-339,524-535
3m1v B:6-13,207-227,229-247,427-443
3m1v E:6-13,207-227,229-247,427-443
3m1v D:71-75,299-326,330-339,524-535
3puf A:44-54,53-64,72-87,172-193
3puf M:44-54,53-64,72-87,172-193
3puf G:44-54,53-64,72-87,172-193
3kjg A:30-36,62-71,82-91,112-132
3kjg B:30-36,62-71,81-91,113-132
3e8j B:122-134,138-157,195-224,285-298
3e8j A:122-134,138-157,195-224,285-298
3p5j A:44-54,56-64,72-87,173-202
3m2v D:71-75,299-326,330-339,524-535
3m2v A:71-75,299-326,330-339,524-535
3m2v B:6-13,207-227,229-247,427-443
3m2v E:6-13,207-227,229-247,427-440
3lew A:79-83,366-382,407-424,427-437
3jro A:1208-1214,1467-1486,1487-1498,1500-1516
3k0e A:39-47,118-138,146-154,156-175
3ez9 A:146-153,174-182,184-194,257-268
3ez9 B:146-153,174-182,184-194,257-268
2zbm A:202-208,211-218,220-234,266-278
2xqy E:158-167,242-261,262-288,291-314
2xqy A:158-167,242-261,262-288,291-314
2dff A:17-27,26-37,45-60,138-164
2dr3 F:23-30,112-128,136-145,144-163
3rc3 A:257-262,604-613,621-646,651-673
3izv J:2-11,14-33,67-82,119-127
3m32 A:71-75,299-326,330-339,524-535
3m32 E:6-13,207-227,229-247,427-443
3m32 D:71-75,299-326,330-339,524-535
3m32 B:6-13,207-227,229-247,427-443
3ez7 A:145-151,173-181,183-192,256-267
3asm A:107-117,116-127,142-151,235-261
3ezf A:146-153,174-182,184-194,257-268
3muo A:14-22,537-552,566-574,589-600
3taz A:77-88,154-184,190-204,262-290
2vsw B:25-31,51-61,64-73,102-116
2vsw A:25-31,51-61,64-74,102-116
2du2 D:3140-3146,3150-3165,3195-3202,3223-3235
3iuq A:14-22,537-552,566-574,589-600
3b8c B:324-330,539-546,550-559,565-580
3b8c A:324-330,539-546,550-559,565-580
3ejo B:121-134,138-157,195-224,285-298
3ejo A:122-134,138-157,195-224,285-298
3tai A:77-88,154-184,190-204,262-290
2d0b A:107-117,116-127,142-151,235-261
3l22 A:78-82,349-365,396-413,415-426
3kji A:30-36,62-71,81-91,112-131
2z72 A:202-208,211-218,220-234,266-278
2ooy G:67-74,90-101,101-113,233-244