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.

Contents

All alpha proteins - SCOPe Class a[edit | edit source]

Mainly helices

DNA/RNA-binding 3-helical bundle[edit | edit source]

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

Homeodomain-like[edit | edit source]

Homeodomain Puzzle 476, Puzzle 481, Puzzle 696

Myb/SANT domain[edit | edit source]

Puzzle 671, Puzzle 685, Puzzle 692

ARID-like[edit | edit source]

Puzzle 698

Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex[edit | edit source]

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

VHP, Villin headpiece domain[edit | edit source]

3 short helices; irregular array

VHP[edit | edit source]

VHP Chicken villin

Histone-fold[edit | edit source]

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

Histone Fold[edit | edit source]

Nucleosome core histones[edit | edit source]

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

4 helical up and down bundle[edit | edit source]

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

Cytochromes[edit | edit source]

Puzzle 711

Alpha-catenin/vinculin-like  [edit | edit source]

Puzzle 458

4-helical cytokines[edit | edit source]

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

Acyl carrier protein-like[edit | edit source]

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

Retrovirus capsid dimerization domain-like[edit | edit source]

Puzzle 744

Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit[edit | edit source]

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

EF Hand-like[edit | edit source]

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

PTS-regulatory domain, PRD[edit | edit source]

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

All beta proteins - SCOPe Class b[edit | edit source]

mainly sheets

OB fold[edit | edit source]

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

Nucleic acid-binding proteins[edit | edit source]

Cold Shock

BC4932-like[edit | edit source]

Puzzle 451

Immunoglobulin-like beta-sandwich[edit | edit source]

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

Immunoglobulin[edit | edit source]

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

C1 set domains (antibody constant domain-like) [edit | edit source]

Puzzle 477

Fibronectin type III[edit | edit source]

Puzzle 491, Puzzle 505, Puzzle 507

PKD domain[edit | edit source]

Puzzle 770 (close to 1BR4), Puzzle 788

Transglutaminase, two C-terminal domains[edit | edit source]

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

ApaG-like[edit | edit source]

Puzzle 408, Puzzle 433, Puzzle 435, Puzzle 442

E set domains[edit | edit source]

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

Invasin/intimin cell-adhesion fragments[edit | edit source]

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

C2 domain-like[edit | edit source]

sandwich; 8 strands in 2 sheets; greek-key

PHL pollen allergen[edit | edit source]

Puzzle 492, Puzzle 497

gamma-Crystallin-like[edit | edit source]

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

Supersandwich[edit | edit source]

Puzzle 511, Puzzle 516, Puzzle 518

SH3-like barrel[edit | edit source]

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

SH3-domain[edit | edit source]

Puzzle 704

PDZ domain-like[edit | edit source]

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

Lipocalins[edit | edit source]

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

Fatty acid binding protein-like[edit | edit source]

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 | edit source]

core: 3-stranded meander beta-sheet 

WW domain[edit | edit source]

Puzzle 415, Puzzle 420

Beta clip[edit | edit source]

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

AFP III-like domain[edit | edit source]

duplication: consists of two structural repeats related by pseudo dyad 

Type III antifreeze protein, AFP III[edit | edit source]

Puzzle 777

Alpha and beta proteins (a+b) - SCOPe Class d[edit | edit source]

Mainly antiparallel beta sheets (segregated alpha and beta regions)

Lysozyme-like[edit | edit source]

common alpha+beta motif for the active site region

Lysozyme-like[edit | edit source]

C-type lysozyme Turkey_Egg_Lysozyme

 IL8-like[edit | edit source]

beta(3)-alpha

Interleukin 8-like chemokines[edit | edit source]

Viral_Macrophage_Inflammatory_Protein

DNA-binding domain[edit | edit source]

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

Dodecin subunit-like[edit | edit source]

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

 Amyloid beta a4 protein copper binding domain (domain 2) [edit | edit source]

Copper Ion Binding

beta-Grasp (ubiquitin-like)[edit | edit source]

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

2Fe-2S ferredoxin-like[edit | edit source]

Puzzle 736

Cystatin-like[edit | edit source]

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

Cystatin/monellin[edit | edit source]

Puzzle 573, Puzzle 580 Cystatins  Potato_Multicystatin

 dsRBD-like[edit | edit source]

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

Alpha-lytic protease prodomain-like[edit | edit source]

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

Fe-S cluster assembly (FSCA) domain-like[edit | edit source]

 NifU C-terminal domain-like[edit | edit source]

Puzzle 693, Puzzle 699

GroEL-intermediate domain like[edit | edit source]

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

Ferredoxin-like[edit | edit source]

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

HMA, heavy metal-associated domain[edit | edit source]

Puzzle 785

Killer toxin KP6 alpha-subunit[edit | edit source]

Killer Toxin

RNA-binding domain, RBD[edit | edit source]

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

Acylphosphatase/BLUF domain-like[edit | edit source]

Acylphosphatase-like Puzzle 506

Probable bacterial effector-binding domain[edit | edit source]

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

Probable bacterial effector-binding domain[edit | edit source]

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

Secretion chaperone-like[edit | edit source]

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

Type III secretory system chaperone-like[edit | edit source]

Type III secretory system chaperone[edit | edit source]

Puzzle 456, Puzzle 472

beta-Grasp (ubiquitin-like)[edit | edit source]

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

Immunoglobulin-binding domains[edit | edit source]

Streptococcal_Protein

Pili subunits[edit | edit source]

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

Pili subunits[edit | edit source]

Puzzle 470

Profilin-like[edit | edit source]

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

PYP-like sensor domain (PAS domain)[edit | edit source]

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

GYF/BRK domain-like[edit | edit source]

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

GYF domain[edit | edit source]

Puzzle 729

TBP-like[edit | edit source]

Puzzle 411

Bet v1-like[edit | edit source]

Puzzle 613

Protein kinase-like (PK-like)[edit | edit source]

Puzzle 478

gpW/XkdW-like[edit | edit source]

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

SufE/NifU[edit | edit source]

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 c[edit | edit source]

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

The "swivelling" beta/beta/alpha domain[edit | edit source]

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 like[edit | edit source]

GroEL-like chaperone, apical domain Puzzle 412

Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)[edit | edit source]

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

Flavodoxin-like[edit | edit source]

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

CheY-like[edit | edit source]

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

CheY-related[edit | edit source]

Puzzle 483

SGNH hydrolase[edit | edit source]

Puzzle 584, Puzzle 588

Phosphotyrosine protein phosphatases I-like[edit | edit source]

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

 PTS system IIB component-like[edit | edit source]

Puzzle 658Puzzle 700

Thioredoxin fold[edit | edit source]

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

Thioredoxin-like[edit | edit source]

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

Thioltransferase[edit | edit source]

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

Txnl5-like [edit | edit source]

Puzzle 457, Puzzle 463Puzzle 480, Puzzle 486

Nucleotide-diphospho-sugar transferases[edit | edit source]

Puzzle 618

Membrane and cell surface proteins and peptides - SCOPe Class f[edit | edit source]

Family A G protein-coupled receptor-like[edit | edit source]

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 g[edit | edit source]

Insulin-like[edit | edit source]

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

Knottins (small inhibitors, toxins, lectins)[edit | edit source]

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

Scorpion toxin-like[edit | edit source]

Short-chain scorpion toxins Scorpion_Toxin, Puzzle 762

Defensin-like[edit | edit source]

Disulfide-rich fold, nearly all-beta

Defensin-like[edit | edit source]

Puzzle 548, Puzzle 624Platypus Venom, Puzzle 774

Crambin-like[edit | edit source]

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

FYVE/PHD zinc finger[edit | edit source]

Puzzle 615

Coiled coil proteins - SCOPe Class h[edit | edit source]

Parallel coiled-coil[edit | edit source]

Coiled-coil dimerization domain from cortexillin I[edit | edit source]

Puzzle 479

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