Research workbench
Structure of yeast complex III with isoform-2 cytochrome C bound and definition of a minimal core interface for electron transfer.
Analyse Structure of yeast complex III with isoform-2 cytochrome C bound and definition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CXH
- Type
- protein
- Length
- 4,472 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B-C1 complex subunit 1, mitochondrial; Cytochrome B-C1 complex subunit 2…
- EC
- 1.10.2.2
- UniProt
- P07256, P07257, P00163, P07143, P08067, P00127, P00128, P08525, P22289, P00045
- Ligands
- HEM, UMQ, SMA, 8PE, CN6, 9PE, 7PH, FES, 6PH, GLC, FRU
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 12 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Cytochrome B-C1 complex subunit 1, mitochondrial (EC 1.10.2.2) | protein | 431 | 45% helix, 18% strand | P07256 |
| B, M | Cytochrome B-C1 complex subunit 2, mitochondrial (EC 1.10.2.2) | protein | 352 | 41% helix, 21% strand | P07257 |
| C, N | Cytochrome B (EC 1.10.2.2) | protein | 385 | 72% helix, 2% strand | P00163 |
| D, O | Cytochrome C1, heme protein, mitochondrial (EC 1.10.2.2) | protein | 246 | 39% helix, 7% strand | P07143 |
| E, P | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 185 | 24% helix, 22% strand | P08067 |
| F, Q | Cytochrome B-C1 complex subunit 6 (EC 1.10.2.2) | protein | 74 | 73% helix, 0% strand | P00127 |
| G, R | Cytochrome B-C1 complex subunit 7 (EC 1.10.2.2) | protein | 125 | 70% helix, 0% strand | P00128 |
| H, S | Cytochrome B-C1 complex subunit 8 (EC 1.10.2.2) | protein | 93 | 44% helix, 10% strand | P08525 |
| I, T | Cytochrome B-C1 complex subunit 9 (EC 1.10.2.2) | protein | 55 | 73% helix, 0% strand | P22289 |
| J, U | Heavy chain (vh) of fv-fragment | protein | 127 | 2% helix, 52% strand | — |
| K, V | Light chain (vl) of fv-fragment | protein | 107 | 3% helix, 38% strand | — |
| W | Cytochrome C iso-2 | protein | 112 | 38% helix, 2% strand | P00045 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 7 copies · chains C, D, N, O, W
- UMQ · Undecyl-maltoside · ligand · 2 copies · chains A, E, H, I, L, P, S, T
- SMA · Stigmatellin A · ligand · 2 copies · chains C, P, E, N
- 8PE · (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate · ligand · 2 copies · chains C, G, H, N, R, S
- CN6 · (2R,5R,11S,14R)-2-(butanoyloxy)-5,8,11-trihydroxy-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate · ligand · 2 copies · chains C, D, G, H, N, O, R, S
- 9PE · (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate · ligand · 2 copies · chains C, N
- 7PH · (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate · ligand · 2 copies · chains C, D, E, N, O, P, T
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, P
- 6PH · (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate · ligand · 2 copies · chains A, C, D, E, L, N, O, P
- GLC · alpha-D-glucopyranose · sugar · chains O, W
- FRU · beta-D-fructofuranose · sugar · chains O, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.85 | 0.87 | 112 | GLC, FRU, HEM |
| 2 | 707 | 0.84 | 0.88 | 69 | HEM |
| 3 | 1190 | 0.83 | 0.84 | 127 | HEM |
| 4 | 170 | 0.82 | 0.97 | 32 | empty |
| 5 | 165 | 0.82 | 0.97 | 31 | empty |
Interfaces
67 interfaces between chains.
- N–R · 1840 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 1807 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1725 Ų buried · 15 hydrogen bonds · protein-protein
- N–O · 1720 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1583 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 cofactor, 1 modified (disulfide, heme attachment, methylation).
Compared structures
- 3CXH · Structure of yeast complex III with isoform-2 cytochrome c bound and definition of a… · the same entry in another collection · chain K against K, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P07256
- Every structure of UniProt P07257
- Every structure of UniProt P00163
- Every structure of UniProt P07143
- Every structure of UniProt P08067
- Every structure of UniProt P00127
- Every structure of UniProt P00128
- Every structure of UniProt P08525
- Every structure of UniProt P22289
- Every structure of UniProt P00045
- Elsewhere: RCSB PDB 3CXH · PDBe 3CXH · UniProt P07256 · UniProt P07257 · UniProt P00163 · UniProt P07143 · UniProt P08067 · UniProt P00127 · UniProt P00128 · UniProt P08525 · UniProt P22289 · UniProt P00045
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.