Domain ID e2ybbd1

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  • A: alpha arrays
  • X: Cytochrome c-like
  • H: Cytochrome c
  • T: Cytochrome c
  • F: Cytochrom_C1
UID: 000431920
Type: Automatic domain
Parent: e1ppjD1
Range: d:1-195
Ligands: HEC
PDB: 2ybb
PDB Description: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL
UniProt: P00125
Hsap BLAST neighbor: P08574
Species: Bos taurus

Structure of domain e2ybbd1

Domains in the same chain:

e2ybbd1 d:1-195 Cytochrome c-like Cytochrome c Cytochrome c
e2ybbd2 d:196-241 cytochrome c1 transmembrane anchor cytochrome c1 transmembrane anchor cytochrome c1 transmembrane anchor

Domains in the same PDB:

e2ybb13 1:2-249 Nqo1 FMN-binding domain-like Nqo1 FMN-binding domain-like Nqo1 FMN-binding domain-like
e2ybb12 1:250-333 beta-Grasp Ubiquitin-related Nqo1 middle domain-like
e2ybb11 1:334-438 Bromodomain-like Nqo1C-terminal domain-like Nqo1C-terminal domain-like
e2ybb22 2:2-74 NQO2 helical bundle domain NQO2 helical bundle domain NQO2 helical bundle domain
e2ybb21 2:75-180 Thioredoxin-like Thioredoxin-like Thioredoxin-like
e2ybb34 3:1-95 beta-Grasp Ubiquitin-related Ubiquitin-like
e2ybb39 3:96-161 iron-sulfur center-binding helical hairpin iron-sulfur center-binding helical hairpin iron-sulfur center-binding helical hairpin
e2ybb37 3:162-246 4Fe-4S ferredoxin 4Fe-4S ferredoxin 4Fe-4S ferredoxin
e2ybb310 3:247-304 Formate dehydrogenase/DMSO reductase, domain 1 Formate dehydrogenase/DMSO reductase, domain 1 Formate dehydrogenase/DMSO reductase, domain 1
e2ybb36 3:305-379,3:542-685 Rossmann-like Formate dehydrogenase/DMSO reductase, domains 2 and 3 Formate dehydrogenase/DMSO reductase, domains 2 and 3
e2ybb35 3:375-541 Rossmann-like Formate dehydrogenase/DMSO reductase, domains 2 and 3 Formate dehydrogenase/DMSO reductase, domains 2 and 3
e2ybb38 3:686-777 cradle loop barrel RIFT-related double psi
e2ybb42 4:25-63,4:378-409 FAD-linked reductases, C-terminal domain-like Ni-Fe binding domain in nickel-iron hydrogenase large subunit Ni-Fe binding domain in nickel-iron hydrogenase large subunit
e2ybb43 4:64-106,4:305-377 FAD-linked reductases, C-terminal domain-like Ni-Fe binding domain in nickel-iron hydrogenase large subunit Ni-Fe binding domain in nickel-iron hydrogenase large subunit
e2ybb41 4:107-304 alpha-helical domain in nickel-iron hydrogenase, large subunit alpha-helical domain in nickel-iron hydrogenase, large subunit alpha-helical domain in nickel-iron hydrogenase, large subunit
e2ybb51 5:1-196 Nqo5-like Nqo5-like Nqo5-like
e2ybb61 6:15-175 Flavodoxin-like Class I glutamine amidotransferase-like CheY-like
e2ybb71 7:3-129 Type III secretory system chaperone-like Frataxin-like Frataxin-like
e2ybb81 8:26-179 4Fe-4S ferredoxin 4Fe-4S ferredoxin 4Fe-4S ferredoxin
e2ybba1 a:1-233 LuxS, MPP, ThrRS/AlaRS common domain LuxS, MPP, ThrRS/AlaRS common domain LuxS/MPP-like metallohydrolase
e2ybba2 a:234-443 LuxS, MPP, ThrRS/AlaRS common domain LuxS, MPP, ThrRS/AlaRS common domain LuxS/MPP-like metallohydrolase
e2ybbA1 A:1-233 LuxS, MPP, ThrRS/AlaRS common domain LuxS, MPP, ThrRS/AlaRS common domain LuxS/MPP-like metallohydrolase
e2ybbA2 A:234-443 LuxS, MPP, ThrRS/AlaRS common domain LuxS, MPP, ThrRS/AlaRS common domain LuxS/MPP-like metallohydrolase
e2ybbb1 b:12-235 LuxS, MPP, ThrRS/AlaRS common domain LuxS, MPP, ThrRS/AlaRS common domain LuxS/MPP-like metallohydrolase
e2ybbb2 b:236-439 LuxS, MPP, ThrRS/AlaRS common domain LuxS, MPP, ThrRS/AlaRS common domain LuxS/MPP-like metallohydrolase
e2ybbB1 B:17-235 LuxS, MPP, ThrRS/AlaRS common domain LuxS, MPP, ThrRS/AlaRS common domain LuxS/MPP-like metallohydrolase
e2ybbB2 B:236-439 LuxS, MPP, ThrRS/AlaRS common domain LuxS, MPP, ThrRS/AlaRS common domain LuxS/MPP-like metallohydrolase
e2ybbc2 c:10-260 Transmembrane heme-binding four-helical bundle Transmembrane heme-binding four-helical bundle Transmembrane di-heme cytochromes
e2ybbc1 c:261-379 a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbC1 C:15-260 Transmembrane heme-binding four-helical bundle Transmembrane heme-binding four-helical bundle Transmembrane di-heme cytochromes
e2ybbC2 C:261-379 a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbd1 d:1-195 Cytochrome c-like Cytochrome c Cytochrome c
e2ybbd2 d:196-241 cytochrome c1 transmembrane anchor cytochrome c1 transmembrane anchor cytochrome c1 transmembrane anchor
e2ybbD1 D:1-195 Cytochrome c-like Cytochrome c Cytochrome c
e2ybbD2 D:196-241 cytochrome c1 transmembrane anchor cytochrome c1 transmembrane anchor cytochrome c1 transmembrane anchor
e2ybbe2 e:1-69 iron-sulfur subunit (ISP) transmembrane anchor iron-sulfur subunit (ISP) transmembrane anchor iron-sulfur subunit (ISP) transmembrane anchor
e2ybbe3 e:70-196 ISP domain ISP domain ISP domain
e2ybbE2 E:1-69 iron-sulfur subunit (ISP) transmembrane anchor iron-sulfur subunit (ISP) transmembrane anchor iron-sulfur subunit (ISP) transmembrane anchor
e2ybbE3 E:70-196 ISP domain ISP domain ISP domain
e2ybbf1 f:12-110 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbF1 F:12-110 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 14 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbg1 g:1-76 Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbG1 G:1-75 Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Ubiquinone-binding protein QP-C of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbh1 h:13-78 cytochrome bc1 complex 11 kDa protein-like Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbH1 H:13-78 cytochrome bc1 complex 11 kDa protein-like Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbi1 i:32-78 Ubiquinol-cytochrome c reductase 8 kDa protein Ubiquinol-cytochrome c reductase 8 kDa protein Ubiquinol-cytochrome c reductase 8 kDa protein
e2ybbI1 I:32-78 Ubiquinol-cytochrome c reductase 8 kDa protein Ubiquinol-cytochrome c reductase 8 kDa protein Ubiquinol-cytochrome c reductase 8 kDa protein
e2ybbj1 j:1-62 Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbJ1 J:1-62 Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbk1 k:15-36 Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbK1 K:15-36 Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Subunit XI (6.4 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
e2ybbL1 L:1-514 Cytochrome c oxidase subunit I-like Cytochrome c oxidase subunit I-like Cytochrome c oxidase subunit I-like
e2ybbM1 M:1-90 Cytochrome c oxidase subunit II-like, transmembrane region Cytochrome c oxidase subunit II-like, transmembrane region Cytochrome c oxidase subunit II-like, transmembrane region
e2ybbM2 M:91-227 Cupredoxin-like Cupredoxin-related Cupredoxin-related
e2ybbN1 N:1-261 Cytochrome c oxidase subunit III-like Cytochrome c oxidase subunit III-like Cytochrome c oxidase subunit III-like
e2ybbO1 O:4-147 Mitochondrial cytochrome c oxidase subunit IV Mitochondrial cytochrome c oxidase subunit IV Mitochondrial cytochrome c oxidase subunit IV
e2ybbP1 P:1-109 Repetitive alpha hairpins Cytochrome c oxidase subunit E Cytochrome c oxidase subunit E
e2ybbQ1 Q:1-98 Rubredoxin-like Rubredoxin-related Cytochrome c oxidase Subunit F
e2ybbR1 R:1-84 Mitochondrial cytochrome c oxidase subunit VIa Mitochondrial cytochrome c oxidase subunit VIa Mitochondrial cytochrome c oxidase subunit VIa
e2ybbS1 S:11-85 Cytochrome c oxidase subunit h Cytochrome c oxidase subunit h Cytochrome c oxidase subunit h
e2ybbT1 T:1-73 Mitochondrial cytochrome c oxidase subunit VIc Mitochondrial cytochrome c oxidase subunit VIc Mitochondrial cytochrome c oxidase subunit VIc
e2ybbU1 U:1-57 Mitochondrial cytochrome c oxidase subunit VIIa Mitochondrial cytochrome c oxidase subunit VIIa Mitochondrial cytochrome c oxidase subunit VIIa
e2ybbV1 V:6-54 Mitochondrial cytochrome c oxidase subunit VIIb Mitochondrial cytochrome c oxidase subunit VIIb Mitochondrial cytochrome c oxidase subunit VIIb
e2ybbW1 W:1-47 Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa)
e2ybbX1 X:1-43 Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX) Mitochondrial cytochrome c oxidase subunit VIIIb (aka IX)
e2ybbY1 Y:1-104 Cytochrome c-like Cytochrome c Cytochrome c

Structural contacts of domain e2ybbd1 of H-group "Cytochrome c":

The domain and its neighboring domains (both within the asymmetric unit and to crystallographic symmetry mates) are represented by spheres and linked by lines. Distances between the center of the domain and interfaces are shown for each contact.

Domain IDSymmetry operatorH-groupVisualization
e2ybbc2 d:X,Y,Z->c:x,y,z Transmembrane heme-binding four-helical bundle Interaction Interface Pymol
e2ybbh1 d:x,y,z->h:X,Y,Z Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Interaction Interface Pymol
e2ybbj1 d:x,y,z->j:X,Y,Z Subunit X (non-heme 7 kDa protein) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Interaction Interface Pymol
e2ybbe2 d:x,y,z->e:X,Y,Z iron-sulfur subunit (ISP) transmembrane anchor Interaction Interface Pymol
e2ybbe2 d:x,y,z->e:X,Y,Z iron-sulfur subunit (ISP) transmembrane anchor Interaction Interface Pymol
e2ybbY1 d:x,y,z->Y:X,Y,Z Cytochrome c Interaction Interface Pymol
e2ybbD1 d:X,Y,Z->D:x,y,z Cytochrome c Interaction Interface Pymol