1SQP: PDB entry 1SQP
Crystal Structure Analysis of Bovine Bc1 with Myxothiazol. Determined by X-ray diffraction at 2.7 Å resolution. Released 1 Nov 2005.
- Method
- X-ray diffraction
- Resolution
- 2.7 Å
- Organism
- Bos taurus
- Chains
- 11
- Atoms
- 17,274
- Mol. weight
- 256.41 kDa
- Ligands
- PLX, FES, MYX, HEC
- Released
- 1 Nov 2005
Explore 1SQP in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1SQP contains 114 α-helices and 62 β-strands across 11 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 26 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-10 | 7 | |
| α-helix | 12-13 | 2 | |
| β-strand | 15-18 | 4 | 1 |
| β-strand | 24-29 | 6 | 1 |
| β-strand | 34-41 | 8 | 1 |
| α-helix | 55-62 | 8 | |
| β-strand | 67 | 1 | 2 |
| α-helix | 74-82 | 9 | |
| β-strand | 85-90 | 6 | 1 |
| β-strand | 95-102 | 8 | 1 |
| α-helix | 103-105 | 3 | |
| α-helix | 106-118 | 13 | |
| β-strand | 120 | 1 | 2 |
| α-helix | 124-141 | 18 | |
| α-helix | 145-157 | 13 | |
| α-helix | 162-164 | 3 | |
| α-helix | 171-176 | 6 | |
| α-helix | 179-189 | 11 | |
| α-helix | 192-194 | 3 | |
| β-strand | 195-201 | 7 | 1 |
| α-helix | 205-215 | 11 | |
| α-helix | 231-233 | 3 | |
| β-strand | 239-245 | 7 | 3 |
| β-strand | 251-259 | 9 | 3 |
| α-helix | 267-277 | 11 | |
| β-strand | 279-281 | 3 | 3 |
| α-helix | 287-289 | 3 | |
| α-helix | 293-300 | 8 | |
| β-strand | 306-314 | 9 | 3 |
| β-strand | 317-326 | 10 | 3 |
| α-helix | 328-330 | 3 | |
| α-helix | 331-348 | 18 | |
| α-helix | 351-368 | 18 | |
| α-helix | 372-385 | 14 | |
| α-helix | 392-400 | 9 | |
| α-helix | 404-414 | 11 | |
| α-helix | 419-420 | 2 | |
| β-strand | 421-426 | 6 | 3 |
| α-helix | 432-433 | 2 | |
| α-helix | 434-439 | 6 | |
Chain B: 20 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-22 | 4 | |
| β-strand | 25-28 | 4 | 4 |
| β-strand | 34-38 | 5 | 4 |
| β-strand | 44-51 | 8 | 4 |
| α-helix | 55-57 | 3 | |
| α-helix | 65-71 | 7 | |
| β-strand | 77 | 1 | 5 |
| β-strand | 80 | 1 | 5 |
| α-helix | 82-92 | 11 | |
| β-strand | 95-100 | 6 | 4 |
| β-strand | 105-112 | 8 | 4 |
| α-helix | 113-115 | 3 | |
| α-helix | 116-128 | 13 | |
| β-strand | 130 | 1 | 5 |
| α-helix | 134-152 | 19 | |
| α-helix | 155-167 | 13 | |
| β-strand | 168 | 1 | 6 |
| α-helix | 180-182 | 3 | |
| α-helix | 188-198 | 11 | |
| α-helix | 201-203 | 3 | |
| β-strand | 204-209 | 6 | 4 |
| α-helix | 213-223 | 11 | |
| β-strand | 239 | 1 | 6 |
| β-strand | 242-247 | 6 | 7 |
| β-strand | 252-260 | 9 | 7 |
| α-helix | 267-279 | 13 | |
| β-strand | 285 | 1 | 1 |
| α-helix | 294-300 | 7 | |
| β-strand | 307-315 | 9 | 7 |
| β-strand | 320-329 | 10 | 7 |
| α-helix | 330-332 | 3 | |
| α-helix | 333-348 | 16 | |
| α-helix | 354-371 | 18 | |
| α-helix | 375-388 | 14 | |
| α-helix | 395-404 | 10 | |
| α-helix | 407-418 | 12 | |
| β-strand | 422-428 | 7 | 7 |
Chain C: 23 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| α-helix | 11-14 | 4 | |
| α-helix | 15-19 | 5 | |
| β-strand | 22-24 | 3 | 8 |
| α-helix | 29-31 | 3 | |
| α-helix | 33-52 | 20 | |
| α-helix | 59-72 | 14 | |
| α-helix | 76-104 | 29 | |
| α-helix | 106-108 | 3 | |
| α-helix | 110-132 | 23 | |
| β-strand | 136 | 1 | 9 |
| α-helix | 137-148 | 12 | |
| α-helix | 149-152 | 4 | |
| α-helix | 157-165 | 9 | |
| α-helix | 172-201 | 30 | |
| β-strand | 217-219 | 3 | 8 |
| α-helix | 220-244 | 25 | |
| α-helix | 253-256 | 4 | |
| β-strand | 258 | 1 | 9 |
| α-helix | 272-283 | 12 | |
| α-helix | 287-299 | 13 | |
| α-helix | 300-302 | 3 | |
| α-helix | 304-307 | 4 | |
| β-strand | 312 | 1 | 10 |
| α-helix | 319-339 | 21 | |
| α-helix | 345-360 | 16 | |
| α-helix | 361-365 | 5 | |
| α-helix | 366-376 | 11 | |
Chain D: 15 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-21 | 3 | |
| α-helix | 23-34 | 12 | |
| α-helix | 37-39 | 3 | |
| β-strand | 47 | 1 | 11 |
| α-helix | 49-51 | 3 | |
| β-strand | 52 | 1 | 12 |
| β-strand | 56 | 1 | 12 |
| α-helix | 58-65 | 8 | |
| β-strand | 69-72 | 4 | 13 |
| α-helix | 73-74 | 2 | |
| β-strand | 81-84 | 4 | 13 |
| α-helix | 85-86 | 2 | |
| α-helix | 89 | 1 | |
| β-strand | 90 | 1 | 11 |
| α-helix | 91-92 | 2 | |
| α-helix | 98-103 | 6 | |
| α-helix | 110-112 | 3 | |
| α-helix | 124-132 | 9 | |
| α-helix | 136-138 | 3 | |
| β-strand | 171 | 1 | 14 |
| β-strand | 175 | 1 | 14 |
| α-helix | 179-190 | 12 | |
| α-helix | 198-231 | 34 | |
| β-strand | 234-237 | 4 | 3 |
Chain E: 10 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-4 | 3 | |
| α-helix | 6-9 | 4 | |
| β-strand | 14 | 1 | 15 |
| α-helix | 16-18 | 3 | |
| α-helix | 26-63 | 38 | |
| α-helix | 66-69 | 4 | |
| β-strand | 76 | 1 | 16 |
| β-strand | 86 | 1 | 17 |
| β-strand | 89 | 1 | 17 |
| β-strand | 96-100 | 5 | 17 |
| α-helix | 106-110 | 5 | |
| α-helix | 124-126 | 3 | |
| β-strand | 132-136 | 5 | 17 |
| α-helix | 146 | 1 | |
| β-strand | 147-148 | 2 | 18 |
| β-strand | 156-158 | 3 | 18 |
| β-strand | 163-165 | 3 | 18 |
| β-strand | 171-173 | 3 | 18 |
| α-helix | 179 | 1 | |
| α-helix | 181 | 1 | |
| β-strand | 185-187 | 3 | 16 |
| β-strand | 193-195 | 3 | 16 |
Chain F: 8 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-24 | 12 | |
| α-helix | 27-29 | 3 | |
| α-helix | 33-35 | 3 | |
| β-strand | 37 | 1 | 10 |
| α-helix | 41-49 | 9 | |
| α-helix | 52-71 | 20 | |
| α-helix | 77-79 | 3 | |
| α-helix | 81-82 | 2 | |
| α-helix | 91-107 | 17 | |
Chain G: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11-18 | 8 | 3 |
| β-strand | 23 | 1 | 15 |
| α-helix | 33-70 | 38 | |
Chain H: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-25 | 10 | |
| α-helix | 28-44 | 17 | |
| α-helix | 55-72 | 18 | |
3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor | A | protein | 480 | Bos taurus | P31800 (AlphaFold model) |
| Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor | B | protein | 453 | Bos taurus | P23004 (AlphaFold model) |
| Cytochrome b | C | protein | 379 | Bos taurus | P00157 (AlphaFold model) |
| Cytochrome c1, heme protein, mitochondrial | D | protein | 241 | Bos taurus | P00125 (AlphaFold model) |
| Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2)… | E | protein | 196 | Bos taurus | P13272 |
| sub6 | F | protein | 110 | Bos taurus | P00129 |
| Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C | G | protein | 81 | Bos taurus | P13271 |
| Ubiquinol-cytochrome c reductase complex 11 kDa protein | H | protein | 78 | Bos taurus | P00126 |
| Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2)… | I | protein | 78 | Bos taurus | P13272 |
| Ubiquinol-cytochrome c reductase complex 7.2 kDa protein | J | protein | 62 | Bos taurus | P00130 |
| Ubiquinol-cytochrome c reductase complex 6.4 kDa protein | K | protein | 56 | Bos taurus | P07552 |
Sequence of entity 1 (A), FASTA
>1SQP_1 Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor (chains A)
MAASAVCRAAGAGTRVLLRTRRSPALLRSSDLRGTATYAQALQSVPETQVSQLDNGLRVA
SEQSSQPTCTVGVWIDAGSRYESEKNNGAGYFVEHLAFKGTKNRPGNALEKEVESMGAHL
NAYSTREHTAYYIKALSKDLPKAVELLADIVQNCSLEDSQIEKERDVILQELQENDTSMR
DVVFNYLHATAFQGTPLAQSVEGPSENVRKLSRADLTEYLSRHYKAPRMVLAAAGGLEHR
QLLDLAQKHFSGLSGTYDEDAVPTLSPCRFTGSQICHREDGLPLAHVAIAVEGPGWAHPD
NVALQVANAIIGHYDCTYGGGAHLSSPLASIAATNKLCQSFQTFNICYADTGLLGAHFVC
DHMSIDDMMFVLQGQWMRLCTSATESEVLRGKNLLRNALVSHLDGTTPVCEDIGRSLLTY
GRRIPLAEWESRIAEVDARVVREVCSKYFYDQCPAVAGFGPIEQLPDYNRIRSGMFWLRF
Sequence of entity 2 (B), FASTA
>1SQP_2 Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (chains B)
MKLLTRAGSLSRFYSLKVAPKVKATEAPAGVPPHPQDLEFTRLPNGLVIASLENYAPASR
IGLFIKAGSRYENSNNLGTSHLLRLASSLTTKGASSFKITRGIEAVGGKLSVTSTRENMA
YTVECLRDDVDILMEFLLNVTTAPEFRRWEVAALQPQLRIDKAVALQNPQAHVIENLHAA
AYRNALANSLYCPDYRIGKVTPVELHDYVQNHFTSARMALIGLGVSHPVLKQVAEQFLNI
RGGLGLSGAKAKYHGGEIREQNGDSLVHAALVAESAAIGSAEANAFSVLQHVLGAGPHVK
RGSNATSSLYQAVAKGVHQPFDVSAFNASYSDSGLFGFYTISQAASAGDVIKAAYNQVKT
IAQGNLSNPDVQAAKNKLKAGYLMSVESSEGFLDEVGSQALAAGSYTPPSTVLQQIDAVA
DADVINAAKKFVSGRKSMAASGNLGHTPFIDEL
Sequence of entity 3 (C), FASTA
>1SQP_3 Cytochrome b (chains C)
MTNIRKSHPLMKIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTT
TAFSSVTHICRDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLETWNIGVILL
LTVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFA
FHFILPFIIMAIAMVHLLFLHETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALM
LLVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILI
LALIPLLHTSKQRSMMFRPLSQCLFWALVADLLTLTWIGGQPVEHPYITIGQLASVLYFL
LILVLMPTAGTIENKLLKW
Sequence of entity 4 (D), FASTA
>1SQP_4 Cytochrome c1, heme protein, mitochondrial (chains D)
SDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLVGVCYTEDE
AKALAEEVEVQDGPNEDGEMFMRPGKLSDYFPKPYPNPEAARAANNGALPPDLSYIVRAR
HGGEDYVFSLLTGYCEPPTGVSLREGLYFNPYFPGQAIGMAPPIYNEVLEFDDGTPATMS
QVAKDVCTFLRWAAEPEHDHRKRMGLKMLLMMGLLLPLVYAMKRHKWSVLKSRKLAYRPP
K
Sequence of entity 5 (E), FASTA
>1SQP_5 Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)] (chains E)
SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS
SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP
QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL
EVPSYEFTSDDMVIVG
Sequence of entity 6 (F), FASTA
>1SQP_6 sub6 (chains F)
AGRPAVSASSRWLEKIRKWYYNAAGFNKLGLMRDDTIHENDDVKEAIRRLPENLYDDRVF
RIKRALDLSMRQQILPKEQWTKYEEDKSYLEPYLKEVIRERKEREEWAKK
Sequence of entity 7 (G), FASTA
>1SQP_7 Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C (chains G)
GRQFGHLTRVRHVITYSLSPFEQRAFPHYFSKGIPNVLRRTRACILRVAPPFVAFYLVYT
WGTQEFEKSKRKNPAAYENDR
Sequence of entity 8 (H), FASTA
>1SQP_8 Ubiquinol-cytochrome c reductase complex 11 kDa protein (chains H)
GDPKEEEEEEEELVDPLTTVREQCEQLEKCVKARERLELCDERVSSRSQTEEDCTEELLD
FLHARDHCVAHKLFNSLK
Sequence of entity 9 (I), FASTA
>1SQP_9 Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)] (chains I)
MLSVAARSGPFAPVLSATSRGVAGALRPLVQAAVPATSESPVLDLKRSVLCRESLRGQAA
GRPLVASVSLNVPASVRY
Sequence of entity 10 (J), FASTA
>1SQP_10 Ubiquinol-cytochrome c reductase complex 7.2 kDa protein (chains J)
VAPTLTARLYSLLFRRTSTFALTIVVGALFFERAFDQGADAIYEHINEGKLWKHIKHKYE
NK
Sequence of entity 11 (K), FASTA
>1SQP_11 Ubiquinol-cytochrome c reductase complex 6.4 kDa protein (chains K)
MLTRFLGPRYRQLARNWVPTAGLWGAVGAVGLVWATDWRLILDWVPYINGKFKKDD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PLX | (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2L… | C42 H89 N O8 P | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 1 |
| MYX | (2Z,6E)-7-{2'-[(2E,4E)-1,6-dimethylhepta-2,4-dienyl]-2,4'-bi-1,3-thiazol-4-yl}-… | C25 H33 N3 O3 S2 | 1 |
| HEC | Heme C | C34 H36 Fe N4 O4 | 3 |
| PEE | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine | C41 H78 N O8 P | 3 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 3 |
Primary citation
Crystallographic studies of quinol oxidation site inhibitors: a modified classification of inhibitors for the cytochrome bc(1) complex. Esser, L., Quinn, B., Li, Y.F. et al. J Mol Biol (2004) 341:281-302. DOI 10.1016/j.jmb.2004.05.065 · PubMed
Other PDB entries of the same protein (UniProt P31800 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1PP9 2.1 Å, Bovine cytochrome bc1 complex with stigmatellin bound
- 1PPJ 2.1 Å, Bovine cytochrome bc1 complex with stigmatellin and antimycin
- 2A06 2.1 Å, Bovine cytochrome bc1 complex with stigmatellin bound
- 9W2X 2.2 Å, Cryo-EM structure of complex III on the bovine heart submitochondrial particles, III-1
- 2FYU 2.26 Å, Crystal structure of bovine heart mitochondrial bc1 with jg144 inhibitor
- 1L0L 2.35 Å, structure of bovine mitochondrial cytochrome bc1 complex with a bound fungicide famoxadone
- 1NTM 2.4 Å, Crystal Structure of Mitochondrial Cytochrome bc1 Complex at 2.4 Angstrom
- 9W2Y 2.4 Å, Cryo-EM structure of complex III on the bovine heart submitochondrial particles, III-2
- 1L0N 2.6 Å, native structure of bovine mitochondrial cytochrome bc1 complex
- 1NTK 2.6 Å, Crystal Structure of Mitochondrial Cytochrome bc1 in Complex with Antimycin A1
- 1NTZ 2.6 Å, Crystal Structure of Mitochondrial Cytochrome bc1 Complex Bound with Ubiquinone
- 1SQX 2.6 Å, Crystal Structure Analysis of Bovine Bc1 with Stigmatellin A
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