Research workbench
Murine supercomplex CIII2CIV in the mature unlocked conformation
Analyse Murine supercomplex CIII2CIV in the mature unlocked conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O3C
- Type
- protein
- Length
- 5,967 residues
- Chains
- 34
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Mus musculus
- Molecule
- Cytochrome b-c1 complex subunit 1, mitochondrial; Cytochrome b-c1 complex subunit 2…
- EC
- 7.1.1.8, 7.1.1.9
- UniProt
- Q9CZ13, Q9DB77, P00158, Q9D0M3, Q9CR68, Q9CQB4, Q9CQ69, P99028, Q8R1I1, Q9CPX8, Q99KD6, P00397, P00405, P00416, P19783, P12787, P19536, P43023, P56391, Q9CPQ1, P56393, P17665, P48772
- Ligands
- 3PE, CDL, HEM, PC1, HEC, FES, HEA, CUA, TGL, CU, NA, MG, ZN
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · resolution 3.3 · 31 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome b-c1 complex subunit 1, mitochondrial | protein | 446 | 45% helix, 19% strand | Q9CZ13 |
| B, M | Cytochrome b-c1 complex subunit 2, mitochondrial | protein | 420 | 44% helix, 20% strand | Q9DB77 |
| C | Cytochrome b | protein | 379 | 70% helix, 2% strand | P00158 |
| D | Cytochrome c1, heme protein, mitochondrial (EC 7.1.1.8) | protein | 241 | 39% helix, 7% strand | Q9D0M3 |
| E, P | Cytochrome b-c1 complex subunit Rieske, mitochondrial (EC 7.1.1.8) | protein | 196 | 26% helix, 19% strand | Q9CR68 |
| F | Cytochrome b-c1 complex subunit 7 | protein | 102 | 63% helix, 0% strand | Q9CQB4 |
| G | Cytochrome b-c1 complex subunit 8 | protein | 74 | 61% helix, 9% strand | Q9CQ69 |
| H, S | Cytochrome b-c1 complex subunit 6, mitochondrial | protein | 68 | 65% helix, 0% strand | P99028 |
| J | Cytochrome b-c1 complex subunit 9 | protein | 58 | 79% helix, 0% strand | Q8R1I1 |
| K | Cytochrome b-c1 complex subunit 10 | protein | 52 | 62% helix, 0% strand | Q9CPX8 |
| L | Cytochrome b-c1 complex subunit 1, mitochondrial | protein | 445 | 44% helix, 19% strand | Q9CZ13 |
| N | Cytochrome b | protein | 380 | 70% helix, 2% strand | P00158 |
| 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 | 65% helix, 0% strand | Q9CQB4 |
| R | Cytochrome b-c1 complex subunit 8 | protein | 72 | 58% helix, 7% strand | Q9CQ69 |
| U | Cytochrome b-c1 complex subunit 9 | protein | 60 | 73% helix, 0% strand | Q8R1I1 |
| V | Cytochrome b-c1 complex subunit 10 | protein | 53 | 60% helix, 0% strand | Q9CPX8 |
| T | Cytochrome b-c1 complex subunit 9 | protein | 78 | 10% helix, 18% strand | Q9CR68 |
| I | Cox7a2l protein | protein | 111 | 40% helix, 9% strand | Q99KD6 |
| a | Cytochrome c oxidase subunit 1 (EC 7.1.1.9) | protein | 514 | 69% helix, 1% strand | P00397 |
| b | Cytochrome c oxidase subunit 2 (EC 7.1.1.9) | protein | 227 | 27% helix, 26% strand | P00405 |
| c | Cytochrome c oxidase subunit 3 (EC 7.1.1.9) | protein | 259 | 75% helix, 0% strand | P00416 |
| d | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial | protein | 144 | 49% helix, 3% strand | P19783 |
| e | Cytochrome c oxidase subunit 5A, mitochondrial | protein | 104 | 61% helix, 1% strand | P12787 |
| f | Cytochrome c oxidase subunit 5B, mitochondrial | protein | 95 | 9% helix, 22% strand | P19536 |
| g | Cytochrome c oxidase subunit 6A2, mitochondrial | protein | 75 | 32% helix, 0% strand | P43023 |
| h | Cytochrome c oxidase subunit 6B1 | protein | 79 | 52% helix, 1% strand | P56391 |
| i | Cytochrome c oxidase subunit 6C | protein | 72 | 68% helix, 1% strand | Q9CPQ1 |
| k | Cytochrome c oxidase subunit 7B, mitochondrial | protein | 49 | 53% helix, 0% strand | P56393 |
| l | Cytochrome c oxidase subunit 7C, mitochondrial | protein | 46 | 63% helix, 0% strand | P17665 |
| m | Cytochrome c oxidase subunit 8B, mitochondrial | protein | 43 | 53% helix, 5% strand | P48772 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 15 copies · chains A, C, G, D, E, J, F, L, N, O, R, P, U, Q, a, d, c, k, m, b, i, f, g
- CDL · Cardiolipin · ligand · 7 copies · chains A, C, K, F, G, D, L, N, V, Q, R, O, E, J, g
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, N
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 3 copies · chains A, D, E, J, K, L, O, P, U, c, g
- HEC · Heme C · ligand · 2 copies · chains D, P, E, O
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, P
- HEA · Heme-A · ligand · 2 copies · chains a, b
- CUA · Dinuclear copper ion · ligand · chains b
- TGL · Tristearoylglycerol · ligand · chains a, l
- CU · Copper (II) ion · metal · chains a
- NA · Sodium ion · metal · chains a
- MG · Magnesium ion · metal · chains a, b
- ZN · Zinc ion · metal · chains f
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 | 1063 | 0.91 | 0.93 | 123 | HEA |
| 2 | 1173 | 0.88 | 0.90 | 137 | empty |
| 3 | 446 | 0.87 | 0.94 | 50 | HEM |
| 4 | 718 | 0.86 | 0.90 | 88 | empty |
| 5 | 1046 | 0.85 | 0.86 | 78 | 3PE |
Interfaces
114 interfaces between chains.
- a–b · 3548 Ų buried · 25 hydrogen bonds · protein-protein
- a–c · 2666 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 2128 Ų buried · 30 hydrogen bonds · protein-protein
- L–M · 2075 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1791 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 cofactor, 1 covalent (disulfide, heme c attachment, covalent ligand).
Compared structures
- 7O3C · Murine supercomplex CIII2CIV in the mature unlocked conformation · the same entry in another collection · chain J against J, 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
- Every structure of UniProt Q99KD6
- Every structure of UniProt P00397
- Every structure of UniProt P00405
- Every structure of UniProt P00416
- Every structure of UniProt P19783
- Every structure of UniProt P12787
- Every structure of UniProt P19536
- Every structure of UniProt P43023
- Every structure of UniProt P56391
- Every structure of UniProt Q9CPQ1
- Every structure of UniProt P56393
- Every structure of UniProt P17665
- Every structure of UniProt P48772
- Elsewhere: RCSB PDB 7O3C · PDBe 7O3C · UniProt Q9CZ13 · UniProt Q9DB77 · UniProt P00158 · UniProt Q9D0M3 · UniProt Q9CR68 · UniProt Q9CQB4 · UniProt Q9CQ69 · UniProt P99028 · UniProt Q8R1I1 · UniProt Q9CPX8 · UniProt Q99KD6 · UniProt P00397 · UniProt P00405 · UniProt P00416 · UniProt P19783 · UniProt P12787 · UniProt P19536 · UniProt P43023 · UniProt P56391 · UniProt Q9CPQ1 · UniProt P56393 · UniProt P17665 · UniProt P48772
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