Research workbench
Murine supercomplex CIII2CIV in the intermediate locked conformation
Analyse Murine supercomplex CIII2CIV in the intermediate locked conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O3E
- Type
- protein
- Length
- 5,417 residues
- Chains
- 31
- 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, 7.1.1.9
- UniProt
- Q9CZ13, Q9DB77, P00158, Q9D0M3, Q9CQB4, Q9CQ69, P99028, Q9CR68, Q99KD6, P00397, P00405, P00416, P19783, P12787, P19536, P43023, P56391, Q9CPQ1, P56393, P17665, P48772, Q8R1I1
- Ligands
- 3PE, CDL, HEM, HEC, PC1, HEA, CUA, TGL, CU, NA, MG, ZN
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 28 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 446 | 43% helix, 19% strand | Q9CZ13 |
| B, M | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 420 | 45% helix, 20% strand | Q9DB77 |
| C | Cytochrome B | protein | 380 | 68% helix, 2% strand | P00158 |
| D | Cytochrome C1, heme protein, mitochondrial (EC 7.1.1.8) | protein | 241 | 40% helix, 5% strand | Q9D0M3 |
| F, Q | Cytochrome B-C1 complex subunit 7 | protein | 101 | 62% helix, 0% strand | Q9CQB4 |
| G | Cytochrome B-C1 complex subunit 8 | protein | 67 | 60% helix, 9% strand | Q9CQ69 |
| H | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 67 | 52% helix, 0% strand | P99028 |
| L | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 445 | 44% helix, 19% strand | Q9CZ13 |
| N | Cytochrome B | protein | 380 | 68% helix, 2% strand | P00158 |
| P | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 7.1.1.8) | protein | 15 | 20% helix, 0% strand | Q9CR68 |
| R | Cytochrome B-C1 complex subunit 8 | protein | 72 | 58% helix, 8% strand | Q9CQ69 |
| S | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 64 | 67% helix, 0% strand | P99028 |
| T | Cytochrome B-C1 complex subunit 9 | protein | 78 | 15% helix, 18% strand | Q9CR68 |
| I | COX7A2L protein | protein | 111 | 37% helix, 5% strand | Q99KD6 |
| a | Cytochrome C oxidase subunit 1 (EC 7.1.1.9) | protein | 514 | 70% helix, 1% strand | P00397 |
| b | Cytochrome C oxidase subunit 2 (EC 7.1.1.9) | protein | 227 | 29% helix, 27% strand | P00405 |
| c | Cytochrome C oxidase subunit 3 (EC 7.1.1.9) | protein | 259 | 74% helix, 0% strand | P00416 |
| d | Cytochrome C oxidase subunit 4 isoform 1, mitochondrial | protein | 144 | 51% helix, 3% strand | P19783 |
| e | Cytochrome C oxidase subunit 5A, mitochondrial | protein | 104 | 59% helix, 1% strand | P12787 |
| f | Cytochrome C oxidase subunit 5B, mitochondrial | protein | 95 | 11% helix, 25% strand | P19536 |
| g | Cytochrome C oxidase subunit 6A2, mitochondrial | protein | 75 | 32% helix, 3% strand | P43023 |
| h | Cytochrome C oxidase subunit 6B1 | protein | 79 | 59% helix, 1% strand | P56391 |
| i | Cytochrome C oxidase subunit 6C | protein | 72 | 69% helix, 1% strand | Q9CPQ1 |
| k | Cytochrome C oxidase subunit 7B, mitochondrial | protein | 49 | 51% 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, 0% strand | P48772 |
| J, U | Cytochrome B-C1 complex subunit 9 | protein | 31 | 74% helix, 0% strand | Q8R1I1 |
| O | Cytochrome C1, heme protein, mitochondrial (EC 7.1.1.8) | protein | 240 | 38% helix, 8% strand | Q9D0M3 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 13 copies · chains C, G, F, l, L, N, R, Q, a, c, b, i, d, g, k, m
- CDL · Cardiolipin · ligand · 5 copies · chains C, F, G, D, L, N, Q, R, O
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, N
- HEC · Heme C · ligand · 2 copies · chains D, O
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains L, O, a, b
- HEA · Heme-A · ligand · 2 copies · chains a, b
- CUA · Dinuclear copper ion · ligand · chains b
- TGL · Tristearoylglycerol · ligand · chains G, 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 | 1198 | 0.91 | 0.93 | 120 | HEA, MG |
| 2 | 1135 | 0.89 | 0.90 | 112 | HEM |
| 3 | 781 | 0.87 | 0.89 | 99 | 3PE |
| 4 | 349 | 0.85 | 0.94 | 56 | empty |
| 5 | 639 | 0.85 | 0.89 | 91 | empty |
Interfaces
88 interfaces between chains.
- a–b · 3459 Ų buried · 29 hydrogen bonds · protein-protein
- a–c · 2655 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2174 Ų buried · 30 hydrogen bonds · protein-protein
- L–M · 2071 Ų buried · 18 hydrogen bonds · protein-protein
- N–O · 1794 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 cofactor (disulfide, heme c attachment).
Compared structures
- 7O3E · Murine supercomplex CIII2CIV in the intermediate locked conformation · the same entry in another collection · chain P against P, 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 Q9CQB4
- Every structure of UniProt Q9CQ69
- Every structure of UniProt P99028
- Every structure of UniProt Q9CR68
- 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
- Every structure of UniProt Q8R1I1
- Elsewhere: RCSB PDB 7O3E · PDBe 7O3E · UniProt Q9CZ13 · UniProt Q9DB77 · UniProt P00158 · UniProt Q9D0M3 · UniProt Q9CQB4 · UniProt Q9CQ69 · UniProt P99028 · UniProt Q9CR68 · 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 · UniProt Q8R1I1
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