3NBT: Trimeric cytochrome c from horse heart
Crystal structure of trimeric cytochrome c from horse heart. Determined by X-ray diffraction at 2.1 Å resolution. Released 14 Jul 2010.
- Method
- X-ray diffraction
- Resolution
- 2.1 Å
- Organism
- Equus caballus
- Chains
- 6
- Atoms
- 5,667
- Mol. weight
- 75.97 kDa
- Ligands
- HEC
- Released
- 14 Jul 2010
Explore 3NBT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
3NBT contains 46 α-helices and 12 β-strands across 6 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: 8 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| α-helix | 24-26 | 3 | |
| β-strand | 39 | 1 | 1 |
| α-helix | 50-54 | 5 | |
| α-helix | 57 | 1 | |
| β-strand | 58 | 1 | 1 |
| α-helix | 59 | 1 | |
| α-helix | 61-67 | 7 | |
| α-helix | 71-74 | 4 | |
| α-helix | 88-101 | 14 | |
Chain B: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| α-helix | 24-26 | 3 | |
| α-helix | 38 | 1 | |
| β-strand | 39 | 1 | 2 |
| α-helix | 50-54 | 5 | |
| β-strand | 58 | 1 | 2 |
| α-helix | 61-69 | 9 | |
| α-helix | 71-74 | 4 | |
| α-helix | 88-101 | 14 | |
Chain C: 10 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| α-helix | 24-26 | 3 | |
| α-helix | 38 | 1 | |
| β-strand | 39 | 1 | 3 |
| α-helix | 47-49 | 3 | |
| α-helix | 50-53 | 4 | |
| α-helix | 57 | 1 | |
| β-strand | 58 | 1 | 3 |
| α-helix | 59 | 1 | |
| α-helix | 61-69 | 9 | |
| α-helix | 71-74 | 4 | |
| α-helix | 88-101 | 14 | |
Chain D: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| α-helix | 24-26 | 3 | |
| β-strand | 39 | 1 | 4 |
| α-helix | 50-53 | 4 | |
| β-strand | 58 | 1 | 4 |
| α-helix | 61-69 | 9 | |
| α-helix | 71-74 | 4 | |
| α-helix | 88-101 | 14 | |
Chain E: 8 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| α-helix | 24-26 | 3 | |
| β-strand | 39 | 1 | 5 |
| α-helix | 50-54 | 5 | |
| α-helix | 57 | 1 | |
| β-strand | 58 | 1 | 5 |
| α-helix | 59 | 1 | |
| α-helix | 61-69 | 9 | |
| α-helix | 71-74 | 4 | |
| α-helix | 88-101 | 14 | |
Chain F: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| α-helix | 24-26 | 3 | |
| α-helix | 38 | 1 | |
| β-strand | 39 | 1 | 6 |
| α-helix | 50-53 | 4 | |
| β-strand | 58 | 1 | 6 |
| α-helix | 61-69 | 9 | |
| α-helix | 71-74 | 4 | |
| α-helix | 88-101 | 14 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cytochrome c | A, B, C, D, E, F | protein | 104 | Equus caballus | P00004 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>3NBT_1 Cytochrome c (chains A, B, C, D, E, F)
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWK
EETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| HEC | Heme C | C34 H36 Fe N4 O4 | 6 |
Water and common crystallization additives (PGE, PEG, PG4) are not listed.
Primary citation
Cytochrome c polymerization by successive domain swapping at the C-terminal helix. Hirota, S., Hattori, Y., Nagao, S. et al. Proc Natl Acad Sci U S A (2010) 107:12854-12859. DOI 10.1073/pnas.1001839107 · PubMed
Other PDB entries of the same protein (UniProt P00004 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6K9J 0.98 Å, 0.98 A three-dimensional structure of horse heart cytochrome C at 110K
- 8ZXR 1.6 Å, Crystal structure of Ssr1698 in complex with heme c
- 3O1Y 1.75 Å, Electron transfer complexes: Experimental mapping of the redox-dependent cytochrome c…
- 1WEJ 1.8 Å, IgG1 FAB fragment (of E8 antibody) complexed with horse cytochrome C at 1.8 a resolution
- 3WC8 1.8 Å, Dimeric horse cytochrome c obtained by refolding with desalting method
- 3WUI 1.8 Å, Dimeric horse cytochrome c formed by refolding from molten globule state
- 6K9I 1.8 Å, High-resolution three-dimensional structure of horse heart cytochrome C at room…
- 1HRC 1.9 Å, High-resolution three-dimensional structure of horse heart cytochrome C
- 3O20 1.9 Å, Electron transfer complexes:experimental mapping of the Redox-dependent Cytochrome C…
- 5IY5 2.0 Å, Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom…
- 1CRC 2.08 Å, Cytochrome C at low ionic strength
- 4NFG 2.11 Å, K13R mutant of horse cytochrome c and yeast cytochrome c peroxidase complex
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