Research workbench
Murine CIII2 focus-refined from supercomplex CICIII2
Analyse Murine CIII2 focus-refined from supercomplex CICIII2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O3H
- Type
- protein
- Length
- 4,161 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B-C1 complex subunit 1, mitochondrial; Cytochrome B-C1 complex subunit 2…
- EC
- 7.1.1.8
- UniProt
- Q9CZ13, Q9DB77, P00158, Q9D0M3, Q9CR68, Q9CQB4, Q9CQ69, P99028, Q8R1I1, Q9CPX8
- Ligands
- 3PE, CDL, HEM, HEC, FES, PC1
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 16 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 446 | 46% helix, 18% strand | Q9CZ13 |
| B, M | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 420 | 43% helix, 20% strand | Q9DB77 |
| C, N | Cytochrome B | protein | 380 | 68% helix, 2% strand | P00158 |
| D | Cytochrome C1, heme protein, mitochondrial (EC 7.1.1.8) | protein | 241 | 38% helix, 8% strand | Q9D0M3 |
| E, P | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 7.1.1.8) | protein | 196 | 28% helix, 17% strand | Q9CR68 |
| F | Cytochrome B-C1 complex subunit 7 | protein | 102 | 65% helix, 0% strand | Q9CQB4 |
| G | Cytochrome B-C1 complex subunit 8 | protein | 80 | 51% helix, 9% strand | Q9CQ69 |
| H, S | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 68 | 71% helix, 0% strand | P99028 |
| J, U | Cytochrome B-C1 complex subunit 9 | protein | 60 | 78% helix, 0% strand | Q8R1I1 |
| K | Cytochrome B-C1 complex subunit 10 | protein | 51 | 75% helix, 0% strand | Q9CPX8 |
| L | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 445 | 45% helix, 19% strand | Q9CZ13 |
| O | Cytochrome C1, heme protein, mitochondrial (EC 7.1.1.8) | protein | 240 | 39% helix, 8% strand | Q9D0M3 |
| Q | Cytochrome B-C1 complex subunit 7 | protein | 101 | 68% helix, 0% strand | Q9CQB4 |
| R | Cytochrome B-C1 complex subunit 8 | protein | 76 | 54% helix, 12% strand | Q9CQ69 |
| V | Cytochrome B-C1 complex subunit 10 | protein | 53 | 70% helix, 0% strand | Q9CPX8 |
| T | Cytochrome B-C1 complex subunit 9 | protein | 78 | 10% helix, 18% strand | Q9CR68 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 8 copies · chains A, C, D, G, E, J, F, L, N, R, O, P, U, Q
- CDL · Cardiolipin · ligand · 6 copies · chains A, C, K, F, G, D, L, N, V, O, Q, R
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, N
- HEC · Heme C · ligand · 2 copies · chains D, E, O
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, P
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, D, E, J, K, L, O, P, U
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 | 901 | 0.84 | 0.86 | 110 | empty |
| 2 | 706 | 0.84 | 0.88 | 66 | HEM |
| 3 | 961 | 0.83 | 0.84 | 85 | HEC |
| 4 | 728 | 0.83 | 0.86 | 67 | HEM |
| 5 | 1108 | 0.81 | 0.82 | 109 | HEC |
Interfaces
67 interfaces between chains.
- L–M · 2088 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2065 Ų buried · 27 hydrogen bonds · protein-protein
- N–O · 1763 Ų buried · 17 hydrogen bonds · protein-protein
- M–T · 1752 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1739 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 cofactor (disulfide, heme c attachment).
Compared structures
- 7O3H · Murine CIII2 focus-refined from supercomplex CICIII2 · 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 Q9CZ13
- Every structure of UniProt Q9DB77
- Every structure of UniProt P00158
- Every structure of UniProt Q9D0M3
- Every structure of UniProt Q9CR68
- Every structure of UniProt Q9CQB4
- Every structure of UniProt Q9CQ69
- Every structure of UniProt P99028
- Every structure of UniProt Q8R1I1
- Every structure of UniProt Q9CPX8
- Elsewhere: RCSB PDB 7O3H · PDBe 7O3H · UniProt Q9CZ13 · UniProt Q9DB77 · UniProt P00158 · UniProt Q9D0M3 · UniProt Q9CR68 · UniProt Q9CQB4 · UniProt Q9CQ69 · UniProt P99028 · UniProt Q8R1I1 · UniProt Q9CPX8
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