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. 2015 Aug 20;109(6):1282–1294. doi: 10.1016/j.bpj.2015.07.034

Table 1.

Proteins in gold standard

Protein Name Mb CL PDB_Chain Ref.
Alpha-MGlcDAG synthase Y NA 1Z2T_A (52)
Phospholipase A2 N NA 1POC_A (53)
Cyt. c oxidase sub. 1 Y NA 2OCC_A (54)
Cyt. c oxidase sub. 7A1, mit. Y NA 2OCC_J (54)
Cyt. c oxidase sub. 7C, mit. Y NA 2OCC_L (54)
ADP/ATP translocase 1 Y CDL 1OKC_A (55)
Cyt. b-c1 complex sub. 1, mit. Y CDL 1SQP_A (56)
Cyt. c1, heme protein, mit. Y CDL 1SQP_D, (56),
2A06_D, Q (57)
Cytochrome b Y CDL 2A06_C, P (57)
Adrenodoxin, mit. Y NA 2BT6_A, B (58,59)
ATP synthase sub. beta, mit. Y NA 2CK3_D, E, F (60)
Cyt. b-c1 complex subunit 8 Y CDL 2YBB_G, (61),
1SQP_G (56)
Cholesterol desmolase Y NA 3MZS_A,B,C,D (58,62)
Protein S100-B N NA 3RM1_A (63)
Cyt. c oxidase sub. 6A2, mit. Y CDL 3WG7_G, T (64)
Cyt. c oxidase sub. 3 Y CDL 3WG7_C, P (64)
FDH-N sub. gamma Y CDL 1KQF_C (65)
FDH-N sub. beta Y CDL 1KQG_B (65)
Cyt. c Y NA 3O1Y_A, B, C (66)
Chr. replication initiator prot. DnaA Y NA 1J1V_A (67)
Cyt. b-556 Y CDN 2ACZ_C (68)
DNA topoisomerase 1 N NA 1MW9_X (69)
Cyt. b Y CDL 3TGU_C, P (70)
Mit. ubiquinol-cyt. c reductase ubiquinone-binding prot. qp-c Y CDL 3TGU_G (70)
Mit. cyt. c1, heme protein Y CDL 3TGU_Q (70)
Prohibitin Y NA 1LU7_A (71)
Beta-2-glycoprotein 1 N NA 3OP8_A, B (72,73)
ABC transporter 10 prot. Y CDL 3ZDQ_A (74)
Acyl-CoA thioesterase THEM5 Y NA 4AE7_A (75)
Caspase-8 Y NA 4JJ7_A (76)
Apoptosis regulator BAX Y NA 4BD2_A (77)
Uncharacterized protein Y CDL 4A2N_B (78)
BH3-interacting domain death agonist Y NA 2VOI_B (79,80)
Antigen-presenting glycoprot. CD1d1 Y CD4 3MA7_A, C (81)
Neutral ceramidase N NA 2zws_A (82)
Carnitine/acylcarnitine translocase Y NA 2BMN_A (83)
Reaction center prot. M chain Y CDL 4LWY_M (84)
Reaction center prot. M chain Y CDL 4N7L_M (85)
ADP,ATP carrier prot. 2 Y CDL 4C9G_A (86)
ADP,ATP carrier prot. 3 Y CDL 4C9J_A, B (86)
Cyt. b Y CDL, 1KB9_C, (87),
CN3, 3CX5_N, (88),
CN5 3CX5_C (88)
Cyt. c1, heme prot. mit. Y CDL, 1P84_D, (89),
CN3 3CX5_D (88)
Sapecin N NA 1L4V_A (90)
Malate dehydrogenase, mit. Y NA model (59)
Thiosulfate sulfurtransferase Y NA model (91)
Tafazzin Y NA model (76)
Serine/threonine-prot. kinase N1 Y NA model (92)
Creatine kinase S-type, mit. Y NA model (93)
Mit. glycerol-3-phosphate dehydrogenase Y NA model (94)
NADH dehydrogenase sub. 1 Y NA NA (95)
Phosphate carrier prot mit. Y NA NA (96)
Prot. UPS1, mit. Y NA NA (97)
Prot. UPS2, mit. Y NA NA (97)
Lysocardiolipin acyltransferase 1 Y NA NA (98)
Phospholipid scramblase 3 Y NA NA (99,100)
Stomatin-like prot. 2, mit. Y NA NA (101)
MICOS complex subunit MIC27 Y NA NA (102)
Phospholipid-transporting ATPase IC Y NA NA (103)
Glycerol-3-phosphate acyltransf. 1, mit. Y NA NA (104)
Carbamoyl-phosphate sinthase I Y NA NA (105)
Neoverrucotoxin subunit alpha N NA NA (106)
AMP deaminase 1 isoform M N NA NA (107)

The column Protein name shows the UniProtKB recommended name of the protein. Some records use alternate and short names as provided in UniProtKB for convenience. Recurring words are abbreviated: mit. for mitochondrial, cyt. for cytochrome, sub. for subunit, chr. for chromosomal, prot. for protein, and transf. for transferase. The column Mb indicates if protein is a membrane or nonmembrane protein (Y and N, respectively). CL shows the structure ID(s) of the cardiolipin costructure(s) given in the PDB file of the protein. PDB_chain indicates the chain of the protein’s PDB structure known to interact with cardiolipin. Records of proteins included in the nonredundant cocrystals subset are shown in bold face. Note that the reaction center protein M chain in PDB 4NL7 was excluded from this subset because it is 100% identical to reaction center protein M chain in PDB 4LWY, although both proteins are from different organisms.