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The SCOPe (Structural Classification of Proteins — extended) database classifies proteins according to their overall shape. Unfortunately, the SCOPe database, which is maintained by the University of California - Berkeley, is scheduled to be shut down in the summer of 2017 due to lack of funding.

This page attempts to categorize Foldit proteins according to the SCOPe classes. In sections below, puzzles shown on the same line involve proteins which should fold to a similar shape.

This page is not being actively maintained as of February 2017.

3D images and distance maps for many proteins from these classes are shown at Distance Maps and http://memorize.com/protein-distance-maps.

For complete lists of player-submitted images of puzzle results, see puzzle results - 379 to 1000 and puzzle results - 1001 and up.

All alpha proteins - SCOPe Class aEdit

Mainly helices

DNA/RNA-binding 3-helical bundleEdit

core: 3-helices; bundle, closed or partly opened, right-handed twist; up-and down 

Homeodomain-likeEdit

Homeodomain Puzzle 476, Puzzle 481, Puzzle 696

Myb/SANT domainEdit

Puzzle 671, Puzzle 685, Puzzle 692

ARID-likeEdit

Puzzle 698

Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complexEdit

3 helices; bundle, closed, right-handed twist; up-and-down: Puzzle 768

VHP, Villin headpiece domainEdit

3 short helices; irregular array

VHPEdit

VHP Chicken villin

Histone-foldEdit

3 helices; long middle helix is flanked at each end with shorter ones

Histone FoldEdit

Nucleosome core histonesEdit

form octamers composed of two copies of each of the four histones: Puzzle 761

4 helical up and down bundleEdit

4 helices; bundle, closed or partly opened, left-handed twist; up-and-down 

CytochromesEdit

Puzzle 711

Alpha-catenin/vinculin-like  Edit

Puzzle 458

4-helical cytokinesEdit

core: 4 helices; bundle, closed; left-handed twist; 2 crossover connections: Puzzle 515, Puzzle 520Symmetry_CASP_ROLL_R0007, Puzzle 554

Acyl carrier protein-likeEdit

4 helices, bundle; helix 3 is shorter than others; up-and-down 

Retrovirus capsid dimerization domain-likeEdit

Puzzle 744

Dimerization-anchoring domain of cAMP-dependent PK regulatory subunitEdit

4 helices; bundle, closed, right-handed twist: Puzzle 672

EF Hand-likeEdit

4 helices; array of 2 hairpins, opened: Puzzle 754

PTS-regulatory domain, PRDEdit

core: 4 helices; bundle, closed, right-handed twist; 1 crossover connection: Puzzle 512, Puzzle 634

All beta proteins - SCOPe Class bEdit

mainly sheets

OB foldEdit

barrel, closed or partly opened n=5, S=10 or S=8; greek-key 

Nucleic acid-binding proteinsEdit

Cold Shock

BC4932-likeEdit

Puzzle 451

Immunoglobulin-like beta-sandwichEdit

sandwich; 7 strands in 2 sheets; greek-key: Puzzle 452, Puzzle 462, Puzzle 432, Puzzle 437

ImmunoglobulinEdit

Puzzle 550 V set domains (antibody variable domain-like) Puzzle 474

C1 set domains (antibody constant domain-like) Edit

Puzzle 477

Fibronectin type IIIEdit

Puzzle 491, Puzzle 505, Puzzle 507

PKD domainEdit

Puzzle 770 (close to 1BR4), Puzzle 788

Transglutaminase, two C-terminal domainsEdit

Puzzle 461, Puzzle 464, Puzzle 482, Puzzle 485, Puzzle 542, Puzzle 546

ApaG-likeEdit

Puzzle 408, Puzzle 433, Puzzle 435, Puzzle 442

E set domainsEdit

Filamin repeat (rod domain) Puzzle 447, Puzzle 459, Puzzle 660

Invasin/intimin cell-adhesion fragmentsEdit

Puzzle 414, Puzzle 416, Puzzle 426, Puzzle 429, Puzzle 668

C2 domain-likeEdit

sandwich; 8 strands in 2 sheets; greek-key

PHL pollen allergenEdit

Puzzle 492, Puzzle 497

gamma-Crystallin-likeEdit

Sandwich; 8 strands in 2 sheets; greek-key duplication: has internal pseudo twofold symmetry Puzzle 766

SupersandwichEdit

Puzzle 511, Puzzle 516, Puzzle 518

SH3-like barrelEdit

barrel, partly opened; n*=4, S*=8; meander the last strand is interrupted by a turn of 3-10 helix

SH3-domainEdit

Puzzle 704

PDZ domain-likeEdit

contains barrel, partly opened; n*=4, S*=8; meander; capped by alpha-helix: T-cell_Lymphoma

LipocalinsEdit

barrel, closed or opened; n=8, S=12; meander

Fatty acid binding protein-likeEdit

ten-stranded meander beta-sheet folded upon itself, relates to the common fold by opening the barrel and insertion of beta-hairpin: Puzzle 733

WW domain-like Edit

core: 3-stranded meander beta-sheet 

WW domainEdit

Puzzle 415, Puzzle 420

Beta clipEdit

double-stranded ribbon sharply bent in two places; the ribbon ends form incomplete barrel; jelly-roll 

AFP III-like domainEdit

duplication: consists of two structural repeats related by pseudo dyad 

Type III antifreeze protein, AFP IIIEdit

Puzzle 777

Alpha and beta proteins (a+b) - SCOPe Class dEdit

Mainly antiparallel beta sheets (segregated alpha and beta regions)

Lysozyme-likeEdit

common alpha+beta motif for the active site region

Lysozyme-likeEdit

C-type lysozyme Turkey_Egg_Lysozyme

 IL8-likeEdit

beta(3)-alpha

Interleukin 8-like chemokinesEdit

Viral_Macrophage_Inflammatory_Protein

DNA-binding domainEdit

beta(3)-alpha; 2 layers: alpha/beta: Puzzle 751

Dodecin subunit-likeEdit

beta-alpha-beta(2); 2 layers: alpha/beta; antiparallel beta-sheet: order 132

 Amyloid beta a4 protein copper binding domain (domain 2) Edit

Copper Ion Binding

beta-Grasp (ubiquitin-like)Edit

core: beta(2)-alpha-beta(2); mixed beta-sheet 2143: Puzzle 784

2Fe-2S ferredoxin-likeEdit

Puzzle 736

Cystatin-likeEdit

alpha-beta(4); helix packs against coiled antiparallel beta-sheet: Puzzle 611

Cystatin/monellinEdit

Puzzle 573, Puzzle 580 Cystatins  Potato_Multicystatin

 dsRBD-likeEdit

alpha-beta(3)-alpha; 2 layers: alpha/beta: Puzzle 728, Puzzle 730, Puzzle 732

Alpha-lytic protease prodomain-likeEdit

core: alpha-beta(2)-(alpha)-beta; 2 layers: alpha/beta

Fe-S cluster assembly (FSCA) domain-likeEdit

 NifU C-terminal domain-likeEdit

Puzzle 693, Puzzle 699

GroEL-intermediate domain likeEdit

3-helical bundle packed against 3-stranded mixed beta-sheet: Puzzle 535, Puzzle 544, Puzzle 547

Ferredoxin-likeEdit

alpha+beta sandwich with antiparallel beta-sheet; (beta-alpha-beta)x2 

HMA, heavy metal-associated domainEdit

Puzzle 785

Killer toxin KP6 alpha-subunitEdit

Killer Toxin

RNA-binding domain, RBDEdit

beta(3)-alpha; 2 layers: alpha/beta Canonical RBD Puzzle 417, Puzzle 431

Acylphosphatase/BLUF domain-likeEdit

Acylphosphatase-like Puzzle 506

Probable bacterial effector-binding domainEdit

duplication of beta-alpha-beta(2) motif: antiparallel beta sheet forms barrel (n=6, S=12) 

Probable bacterial effector-binding domainEdit

Gyrase inhibitory protein Gyr Puzzle 438, Puzzle 446, Puzzle 473, Puzzle 498

Secretion chaperone-likeEdit

alpha-beta(3)-alpha-beta(2)-alpha; 2 layers: alpha/beta

Type III secretory system chaperone-likeEdit

Type III secretory system chaperoneEdit

Puzzle 456, Puzzle 472

beta-Grasp (ubiquitin-like)Edit

core: beta(2)-alpha-beta(2); mixed beta-sheet 2143: Puzzle 469

Immunoglobulin-binding domainsEdit

Streptococcal_Protein

Pili subunitsEdit

contains very long N-terminal helix, which end is packed against beta-sheet

Pili subunitsEdit

Puzzle 470

Profilin-likeEdit

2 alpha-helices and 5-stranded antiparallel sheet: order 21543; 3 layers: alpha/beta/alpha 

PYP-like sensor domain (PAS domain)Edit

alpha-beta(2)-alpha(2)-beta(3): Puzzle 517, Puzzle 521, Puzzle 524

GYF/BRK domain-likeEdit

beta(2)-alpha-beta(2)-alpha; 2 layers, alpha/beta

GYF domainEdit

Puzzle 729

TBP-likeEdit

Puzzle 411

Bet v1-likeEdit

Puzzle 613

Protein kinase-like (PK-like)Edit

Puzzle 478

gpW/XkdW-likeEdit

alpha-beta(2)-alpha; antiparallel hairpin: Puzzle 500

SufE/NifUEdit

alpha(2)-beta(3)-alpha(3); 2 layers alpha/beta, 3-stranded antiparallel beta-sheet; order 123: Puzzle 551

Alpha and beta proteins (a/b) - SCOPe Class cEdit

Mainly parallel beta sheets (beta-alpha-beta units)

The "swivelling" beta/beta/alpha domainEdit

3 layers: b/b/a; the central sheet is parallel, and the other one is antiparallel; there are some variations in topology

GroEL apical domain likeEdit

GroEL-like chaperone, apical domain Puzzle 412

Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)Edit

2 curved layers, a/b; parallel beta-sheet; order 1234...N: Puzzle 527, Puzzle 534

Flavodoxin-likeEdit

3 layers, a/b/a; parallel beta-sheet of 5 strand, order 21345

CheY-likeEdit

Puzzle 434, Puzzle 436, Puzzle 440, Puzzle 445, Puzzle 449, Puzzle 453, Puzzle 454, Puzzle 488, Puzzle 502

CheY-relatedEdit

Puzzle 483

SGNH hydrolaseEdit

Puzzle 584, Puzzle 588

Phosphotyrosine protein phosphatases I-likeEdit

3 layers: a/b/a; parallel beta-sheet of 4 strands, order 2134

 PTS system IIB component-likeEdit

Puzzle 658Puzzle 700

Thioredoxin foldEdit

core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest

Thioredoxin-likeEdit

core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest: Puzzle 621

ThioltransferaseEdit

Puzzle 455, Puzzle 622, Puzzle 467, Puzzle 739, Puzzle 746

Txnl5-like Edit

Puzzle 457, Puzzle 463Puzzle 480, Puzzle 486

Nucleotide-diphospho-sugar transferasesEdit

Puzzle 618

Membrane and cell surface proteins and peptides - SCOPe Class fEdit

Family A G protein-coupled receptor-likeEdit

core: up-and-down bundle of seven transmembrane helices tilted 20 degrees with respect to the plane of the membrane: Puzzle 726

Small proteins - SCOPe Class gEdit

Insulin-likeEdit

nearly all-alpha can be classified as disulfide-rich: Puzzle 707

Knottins (small inhibitors, toxins, lectins)Edit

disulfide-bound fold; contains beta-hairpin with two adjacent disulfides 

Scorpion toxin-likeEdit

Short-chain scorpion toxins Scorpion_Toxin, Puzzle 762

Defensin-likeEdit

Disulfide-rich fold, nearly all-beta

Defensin-likeEdit

Puzzle 548, Puzzle 624Platypus Venom, Puzzle 774

Crambin-likeEdit

disulfide-rich alpha+beta fold: Puzzle 781Puzzle 790

FYVE/PHD zinc fingerEdit

Puzzle 615

Coiled coil proteins - SCOPe Class hEdit

Parallel coiled-coilEdit

Coiled-coil dimerization domain from cortexillin IEdit

Puzzle 479

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