1. i.1.1 Ribosome and ribosomal fragments
Ribosome and ribosomal fragments
2zkr d2zkre1 E:101-106,110-116,123-128,150-166,177-183
1w2b d1w2be_ E:93-99,100-106,113-118,137-153,164-172
1sm1 d1sm1e_ E:94-98,102-107,112-116,137-153,160-164
1giy d1giyh_ H:93-99,100-106,111-115,136-152,159-164
1eg0 d1eg0j_ J:87-93,94-100,105-109,130-146,153-158
487d d487dj_ J:93-99,100-106,111-115,136-152,159-164
1c04 d1c04b_ B:93-99,100-106,111-115,136-152,159-164
1ml5 d1ml5h_ H:93-99,100-106,111-115,136-152,159-164
2. d.141.1 Ribosomal protein L6
Ribosomal protein L6 consists of two beta-sheets and one alpha-helix packed around single core
1yjw d1yjwe2 E:93-99,100-106,113-118,137-153,164-172
1yit d1yite2 E:93-99,100-106,113-118,137-153,164-172
1yhq d1yhqe2 E:93-99,100-106,113-118,137-153,164-172
1m1k d1m1kg2 G:93-99,100-106,113-118,137-153,164-172
1vq7 d1vq7e2 E:93-99,100-106,113-118,137-153,164-172
1vqk d1vqke2 E:93-99,100-106,113-118,137-153,164-172
1n8r d1n8rg2 G:93-99,100-106,113-118,137-153,164-172
1vqm d1vqme2 E:93-99,100-106,113-118,137-153,164-172
1yjn d1yjne2 E:93-99,100-106,113-118,137-153,164-172
1m90 d1m90g2 G:93-99,100-106,113-118,137-153,164-172
1vqn d1vqne2 E:93-99,100-106,113-118,137-153,164-172
1k73 d1k73g2 G:93-99,100-106,113-118,137-153,164-172
1k8a d1k8ag2 G:93-99,100-106,113-118,137-153,164-172
1qvf d1qvfe2 E:93-99,100-106,113-118,137-153,164-172
1vqp d1vqpe2 E:93-99,100-106,113-118,137-153,164-172
1k9m d1k9mg2 G:93-99,100-106,113-118,137-153,164-172
1q86 d1q86g2 G:93-99,100-106,113-118,137-153,164-172
1kd1 d1kd1g2 G:93-99,100-106,113-118,137-153,164-172
1nji d1njig2 G:93-99,100-106,113-118,137-153,164-172
1kc8 d1kc8g2 G:93-99,100-106,113-118,137-153,164-172
1jj2 d1jj2e2 E:93-99,100-106,113-118,137-153,164-172
1kqs d1kqse2 E:93-99,100-106,113-118,137-153,164-172
1vq9 d1vq9e2 E:93-99,100-106,113-118,137-153,164-172
2otj d2otje2 E:93-99,100-106,113-118,137-153,164-172
1yj9 d1yj9e2 E:93-99,100-106,113-118,137-153,164-172
1yij d1yije2 E:93-99,100-106,113-118,137-153,164-172
1vql d1vqle2 E:93-99,100-106,113-118,137-153,164-172
1q82 d1q82g2 G:93-99,100-106,113-118,137-153,164-172
1vqo d1vqoe2 E:93-99,100-106,113-118,137-153,164-172
1vq8 d1vq8e2 E:93-99,100-106,113-118,137-153,164-172
1s72 d1s72e2 E:93-99,100-106,113-118,137-153,164-172
1qvg d1qvge2 E:93-99,100-106,113-118,137-153,164-172
1yi2 d1yi2e2 E:93-99,100-106,113-118,137-153,164-172
1vq5 d1vq5e2 E:93-99,100-106,113-118,137-153,164-172
1q81 d1q81g2 G:93-99,100-106,113-118,137-153,164-172
1vq6 d1vq6e2 E:93-99,100-106,113-118,137-153,164-172
1q7y d1q7yg2 G:93-99,100-106,113-118,137-153,164-172
1vq4 d1vq4e2 E:93-99,100-106,113-118,137-153,164-172
2otl d2otle2 E:93-99,100-106,113-118,137-153,164-172
1ffk d1ffk12 1:93-99,100-106,113-118,137-153,164-172
2j03 d2j03h2 H:94-100,101-107,112-117,137-153,160-165
2j01 d2j01h2 H:94-100,101-107,112-117,137-153,160-165
3d5d d3d5dh2 H:94-100,101-107,112-117,137-153,160-165
3d5b d3d5bh2 H:94-100,101-107,112-117,137-153,160-165
1yl3 d1yl3h2 H:93-99,100-106,111-115,136-152,159-164
2b9p d2b9ph2 H:93-99,100-106,111-115,136-152,159-164
2b9n d2b9nh2 H:93-99,100-106,111-115,136-152,159-164
2b66 d2b66h2 H:93-99,100-106,111-115,136-152,159-164
2v49 d2v49h2 H:94-100,101-107,112-117,137-153,160-165
2v47 d2v47h2 H:94-100,101-107,112-117,137-153,160-165
2qov d2qovg2 G:93-99,100-106,111-116,136-152,159-164
2qox d2qoxg2 G:93-99,100-106,111-116,136-152,159-164
1vs8 d1vs8g2 G:93-99,100-106,111-116,136-152,158-164
3cf5 d3cf5e1 E:94-100,101-107,112-117,137-153,160-164
2hgj d2hgjh2 H:93-100,101-107,113-117,137-153,160-165
2i2v d2i2vg2 G:93-99,100-106,111-116,136-152,160-164
2i2t d2i2tg2 G:93-99,100-106,111-116,136-152,160-164
1rl6 d1rl6a2 A:93-99,100-106,111-115,136-152,159-164
2hgu d2hguh2 H:94-100,101-107,113-117,137-153,160-164
2hgq d2hgqh2 H:94-98,101-107,113-117,137-153,160-164
2vhm d2vhmg2 G:92-99,100-107,111-116,136-152,157-164
2qao d2qaog2 G:93-99,100-106,111-116,136-152,157-164
2qam d2qamg2 G:93-99,100-106,111-116,136-152,157-164
2awb d2awbg2 G:93-99,100-106,111-116,136-152,157-164
2j28 d2j28g2 G:93-99,100-106,111-116,136-152,157-164
2rdo d2rdog2 G:93-99,100-106,111-116,136-152,157-164
2aw4 d2aw4g2 G:93-99,100-106,111-116,136-152,157-164
3bbx d3bbxg2 G:93-99,100-106,111-116,136-152,157-164
1vs6 d1vs6g2 G:93-99,100-106,111-116,136-152,157-164
2vhn d2vhng2 G:93-99,100-106,111-116,136-152,157-164
2qbe d2qbeg2 G:93-99,100-106,112-116,136-152,157-164
2qbg d2qbgg2 G:93-99,100-106,112-116,136-152,157-164
2zjr d2zjre1 E:94-100,101-107,112-116,137-153,158-164
2zjp d2zjpe1 E:94-100,101-107,112-116,137-153,158-164
2z4n d2z4ng2 G:94-99,100-105,111-116,136-152,157-164
2z4l d2z4lg2 G:94-99,100-105,111-116,136-152,157-164
3df4 d3df4g2 G:94-99,100-105,111-116,136-152,157-164
3df2 d3df2g2 G:94-99,100-105,111-116,136-152,157-164
3. c.37.1 P-loop containing nucleoside triphosphate hydrolases division into families based on beta-sheet topologies !
P-loop containing nucleoside triphosphate hydrolases 3 layers: a/b/a, parallel or mixed beta-sheets of variable sizes
1g9x d1g9xc_ C:2005-2015,2060-2067,2068-2072,2075-2083,2173-2179
1ji0 d1ji0a_ A:3-16,57-65,66-70,73-81,158-164
1g9x d1g9xc_ C:2005-2015,2060-2067,2068-2072,2075-2083,2083-2087
1g9x d1g9xb_ B:1005-1018,1060-1067,1068-1072,1075-1083,1173-1179
1g6h d1g6ha_ A:5-18,60-67,68-72,75-83,173-179
1gaj d1gaja_ A:5-18,60-67,68-72,75-83,173-179
1ji0 d1ji0a_ A:3-16,57-65,66-70,73-81,81-86
1gaj d1gaja_ A:5-18,60-67,68-72,75-83,83-87
1g6h d1g6ha_ A:5-18,60-67,68-72,75-83,83-87
1g9x d1g9xb_ B:1005-1018,1060-1067,1068-1072,1075-1083,1083-1087
2i3b d2i3ba1 A:34-43,48-54,56-63,83-97,106-115
4. d.10.1 DNA-binding domain
DNA-binding domain beta(3)-alpha; 2 layers: alpha/beta
1ig4 d1ig4a_ A:15-22,30-38,40-44,45-54,61-65
5. b.69.14 Nucleoporin domain
7-bladed beta-propeller consists of seven 4-stranded beta-sheet motifs; meander
1xip d1xipa_ A:41-47,48-56,57-63,63-74,335-343
6. 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
1tau d1taua3 A:305-313,319-329,330-335,337-346,347-351
3ktq d3ktqa1 A:305-313,319-329,330-335,337-345,347-351
7. b.113.1 N-terminal domain of MutM-like DNA repair proteins
N-terminal domain of MutM-like DNA repair proteins pseudobarrel; capped on both ends by alpha-helices
1q39 d1q39a2 A:52-59,61-67,107-112,112-119,125-129
1q3c d1q3ca2 A:52-59,61-67,107-112,112-119,125-129
1q3b d1q3ba2 A:52-59,61-67,107-113,112-119,125-129
8. d.152.1 Aldehyde ferredoxin oxidoreductase, N-terminal domain
Aldehyde ferredoxin oxidoreductase, N-terminal domain contains sandwich; duplication of alpha+beta motif with single mixed sheet ! motif: beta(2)-alpha-beta(3)-alpha-beta; strand order 216345, strands 1 and 6 are parallel
1aor d1aora2 A:58-63,76-84,87-95,188-197,197-205
1aor d1aorb2 B:58-63,76-84,87-95,188-197,197-205
1b4n d1b4nd2 D:57-62,74-81,86-95,186-195,195-203
1b4n d1b4nb2 B:57-62,74-82,86-95,186-195,195-203
1b4n d1b4na2 A:57-62,74-82,87-95,186-195,195-203
1b25 d1b25a2 A:57-62,74-82,87-95,186-195,195-203
1b25 d1b25d2 D:57-62,74-83,86-95,186-195,195-203
1b25 d1b25c2 C:57-62,74-83,86-95,186-195,195-203
1b25 d1b25b2 B:57-62,74-83,86-95,186-195,195-203
1b4n d1b4nc2 C:57-62,74-82,87-95,186-195,195-203
9. b.43.4 Riboflavin synthase domain-like
Reductase/isomerase/elongation factor common domain barrel, closed; n=6, S=10; greek-key
1ewy d1ewyb1 B:58-63,76-82,93-101,159-171,297-303
1gjr d1gjra1 A:58-63,76-82,93-101,159-171,297-303
10. d.338.1 Oxysterol-binding protein-like
Oxysterol-binding protein-like core: large meander beta-sheet of 12 strands wrapped around the N-terminal (distorted) alpha-hairpin; some similarity to transmembrane beta-barrel proteins
1zi7 d1zi7c1 C:175-190,191-198,215-224,382-392,415-422
1zi7 d1zi7b1 B:175-190,191-206,217-224,382-392,416-422
1zi7 d1zi7a1 A:176-190,191-205,212-224,382-392,416-422
1zi7 d1zi7a1 A:146-156,157-172,176-190,382-392,416-422
1zi7 d1zi7c1 C:146-156,157-173,175-190,382-392,415-422
1zhz d1zhza1 A:146-156,157-173,175-190,382-392,416-422
1zhx d1zhxa1 A:146-156,157-173,175-190,382-392,416-422
1zhy d1zhya1 A:146-156,157-173,175-190,382-392,416-422
1zi7 d1zi7b1 B:146-156,157-173,175-190,382-392,416-422
1zht d1zhta1 A:146-156,157-173,175-190,382-392,415-422
1zhw d1zhwa1 A:146-156,157-173,175-190,382-392,416-422
11. b.26.1 SMAD/FHA domain has a few short helices inserted in loops !
SMAD/FHA domain sandwich; 11 strands in 2 sheets; greek-key
1mjs d1mjsa_ A:290-299,300-308,337-343,358-370,392-399
List of motif hits that are not present in SCOP but are found in PDB for pattern ID: 475 (enumeration index: query1105) of S5
3orb G:93-99,100-106,111-116,136-152,157-163
3pyv G:94-100,101-107,112-117,137-153,160-164
3akh A:20-27,29-37,41-49,50-57,294-301
3ofz G:93-99,100-106,111-116,136-152,157-163
3kiy H:94-100,101-107,112-116,137-153,160-164
3i56 E:93-99,100-106,113-118,137-153,164-172
3pio E:94-100,101-107,112-116,137-153,158-165
3izr F:100-107,108-115,122-127,149-165,176-182
2y11 H:94-100,101-107,112-116,137-153,160-164
3izs F:99-105,110-116,123-128,150-166,177-185
3f1h H:94-100,101-107,112-117,137-153,160-164
3ofc G:93-99,100-106,111-116,136-152,157-163
3r8s G:93-99,100-106,111-116,136-152,157-164
3g6e E:93-99,100-106,113-118,137-153,164-172
2oh5 A:34-44,46-56,207-216,216-229,231-235
3i55 E:93-99,100-106,113-118,137-153,164-172
2wrr H:94-100,101-107,112-117,137-153,160-165
3f1f H:94-100,101-107,112-117,137-153,160-164
3e1b 3:93-99,100-106,111-116,136-152,157-164
2y13 H:94-100,101-107,112-116,137-153,160-164
3foa B:234-241,277-286,287-297,310-318,322-326
3foa D:234-241,277-286,287-297,310-318,322-326
3foa C:234-241,277-286,287-297,310-318,322-326
3foa A:234-241,277-286,287-297,310-318,322-326
3aki A:20-27,29-37,41-49,50-57,294-301
3fo8 D:234-240,277-286,287-297,310-318,322-326
2wrl H:94-100,101-107,112-116,137-153,160-164
3hux H:94-100,101-107,112-116,137-153,160-164
2y0v H:94-100,101-107,112-116,137-153,160-164
3i20 G:93-99,100-106,111-116,136-152,157-163
2x9u H:94-100,101-107,112-116,137-153,160-164
2wrj H:94-100,101-107,112-116,137-153,160-164
3akg A:20-27,29-37,41-49,50-57,294-301
3g4s E:93-99,100-106,113-118,137-153,164-172
3ofq G:93-99,100-106,111-116,136-152,158-164
2oh6 A:34-44,46-56,207-216,216-229,231-235
3huz H:94-100,101-107,112-117,137-153,160-164
3ofr G:93-99,100-106,111-116,136-152,157-163
3g71 E:93-99,100-106,113-118,137-153,164-172
3i1t G:93-99,100-105,111-116,136-152,158-164
3oat G:93-99,100-106,111-116,136-152,157-163
3oi3 H:94-100,101-107,112-116,137-153,160-165
3oh7 H:94-100,101-107,112-117,137-153,160-164
3eb8 A:85-94,95-104,105-112,113-124,126-130
3eb8 B:85-94,95-104,105-112,113-124,126-130
3jqp A:52-57,100-106,113-120,179-194,310-316
3ofd G:93-99,100-105,111-116,136-152,158-164
2xtg H:94-100,101-107,112-116,137-153,160-164
2xqe H:94-100,101-107,112-117,137-153,160-164
2wdn H:94-100,101-107,112-116,137-153,160-164
2y0x H:94-100,101-107,112-116,137-153,160-164
3spw A:177-190,191-203,213-224,382-392,416-422
3spw A:146-156,157-171,177-190,382-392,416-422
3spw B:146-156,157-170,178-190,382-392,415-422
3spw B:178-190,191-198,217-224,382-392,415-422
3fik G:93-99,100-106,111-116,136-149,159-164
3mrz G:94-100,101-107,112-117,137-153,160-165
3oi1 H:94-100,101-107,112-117,137-153,160-164
3e1d 3:93-99,100-106,111-116,136-152,157-164
4a17 E:99-104,108-114,121-126,148-164,175-186
3foi F:234-241,277-286,287-297,310-318,322-326
3foi E:234-241,277-286,287-297,310-318,322-326
3foi C:234-241,277-286,287-297,310-318,322-326
3foi D:234-241,277-286,287-297,310-318,322-326
3foi A:234-241,277-286,287-297,310-318,322-326
3foi B:234-241,277-286,287-297,310-318,322-326
3ohz H:94-100,101-107,112-117,137-153,160-164
2nnw C:8-13,14-21,23-30,48-62,65-69
2nnw A:8-13,14-21,23-30,48-62,65-69
4a1c E:99-104,108-114,121-126,148-164,175-186
2wwq G:93-99,100-105,112-116,136-152,159-164
3cxc E:93-99,100-106,113-118,137-153,164-172
3kir H:94-100,101-107,112-116,137-153,160-164
3jyw H:99-104,110-116,123-128,150-166,176-182
3ohj H:94-100,101-107,112-117,137-153,160-164
3k1u A:16-23,25-33,37-45,46-53,294-301
2x9s H:94-100,101-107,112-116,137-153,160-164
3oi5 H:94-100,101-107,112-116,137-153,160-165
1w9z C:140-149,160-170,178-189,205-219,227-232
1w9z A:140-149,160-170,179-189,205-219,227-232
1w9z B:140-149,160-170,179-189,205-219,227-232
3l4n A:127-133,184-189,190-195,205-217,220-224
2y17 H:94-100,101-107,112-116,137-153,160-164
3nmu B:8-13,14-21,23-30,48-62,65-69
3kiw H:94-100,101-107,112-116,137-153,160-164
3pyt G:94-100,101-107,112-117,137-153,160-164
3oh5 H:94-100,101-107,112-117,137-153,160-164
2xux H:94-100,101-107,112-116,137-153,160-164
2wro H:94-100,101-107,112-117,137-153,160-165
3nvm A:8-13,14-21,23-30,48-62,65-69
2oh7 A:34-44,46-56,207-216,216-229,231-235
3pyr G:94-100,101-107,112-117,137-153,160-164
2y15 H:94-100,101-107,112-116,137-153,160-164
3kni H:94-100,101-107,112-117,137-153,160-164
3pyo G:94-100,101-107,112-117,137-153,160-164
3oas G:93-99,100-105,111-116,136-152,158-164
4a1a E:99-104,108-114,121-126,148-164,175-186
3ohk H:94-100,101-107,112-117,137-153,160-164
3kit H:94-100,101-107,112-116,137-153,160-164
3og0 G:93-99,100-105,111-116,136-152,158-164
3i22 G:93-99,100-105,111-116,136-152,158-164
3ms1 G:94-100,101-107,112-117,137-153,160-165
2wdl H:94-100,101-107,112-116,137-153,160-164
3ee1 A:85-94,95-101,109-113,113-125,126-130
3ee1 B:85-94,95-101,109-113,113-125,126-130
3i9e H:94-100,101-107,112-116,137-151,160-165
3rrm C:41-47,48-56,57-63,63-74,372-381
3i1n G:93-99,100-106,111-116,136-152,157-163
3akf A:20-27,29-37,41-49,50-57,294-301
3r8t G:93-99,100-106,111-116,136-152,157-164
2y19 H:94-100,101-107,112-116,137-153,160-164
2y0z H:94-100,101-107,112-116,137-153,160-164
3fin H:94-100,101-107,112-117,137-153,160-165
3foh F:234-241,277-286,287-297,310-318,322-326
3foh E:234-241,277-286,287-297,310-318,322-326
3foh C:234-241,277-286,287-297,310-318,322-326
3foh D:234-241,277-286,287-297,310-318,322-326
3foh A:234-241,277-286,287-297,310-318,322-326
3foh B:234-241,277-286,287-297,310-318,322-326
3i1r G:93-99,100-106,111-116,136-152,157-163
3i1p G:93-99,100-105,111-116,136-152,158-164
2qa4 E:93-99,100-106,113-118,137-153,164-172
3ccs E:93-99,100-106,113-118,137-153,164-172
3ccm E:93-99,100-106,113-118,137-153,164-172
3ccj E:93-99,100-106,113-118,137-153,164-172
3ccr E:93-99,100-106,113-118,137-153,164-172
2qex E:93-99,100-106,113-118,137-153,164-172
3cma E:93-99,100-106,113-118,137-153,164-172
3cme E:93-99,100-106,113-118,137-153,164-172
3ccq E:93-99,100-106,113-118,137-153,164-172
3cc7 E:93-99,100-106,113-118,137-153,164-172
3cc4 E:93-99,100-106,113-118,137-153,164-172
3cpw E:93-99,100-106,113-118,137-153,164-172
3ccu E:93-99,100-106,113-118,137-153,164-172
3ccl E:93-99,100-106,113-118,137-153,164-172
3cce E:93-99,100-106,113-118,137-153,164-172
3cc2 E:93-99,100-106,113-118,137-153,164-172
3bbo I:138-143,144-149,155-160,180-196,201-208
3ccv E:93-99,100-106,113-118,137-153,164-172
3cd6 E:93-99,100-106,113-118,137-153,164-172