MolNFT v1 · #151654 · protein
III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae
6HU9 · Cytochrome B-C1 complex subunit 1, mitochondrial: “III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae”. Electron microscopy, 13 ligands (PEF, CDL, PCF), 20 pockets (best druggability 0.91). MolNFT v1 #151654 on…
- PDB
- 6HU9
- Type
- protein
- Length
- 7,636 residues
- Chains
- 44
- 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
- 1.10.2.2, 1.9.3.1
- UniProt
- P07256, P07257, P00163, P07143, P08067, P00127, P00128, P08525, P22289, P37299, P00401, P00410, P00420, P04037, P00424, P00427, P10174, P04039, P07255, Q01519, P32799, Q2V2P9
- Ligands
- PEF, CDL, PCF, HEM, HEA, HEC, FES, UQ6, CUA, CU, CA, MG, ZN
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 22 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 431 | 42% helix, 18% strand | P07256 |
| B, M | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 352 | 37% helix, 21% strand | P07257 |
| C, N | Cytochrome B | protein | 385 | 71% helix, 3% strand | P00163 |
| D, O | Cytochrome C1, heme protein, mitochondrial | protein | 247 | 40% helix, 7% strand | P07143 |
| E, P | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 185 | 29% helix, 22% strand | P08067 |
| F, Q | Cytochrome B-C1 complex subunit 6 | protein | 75 | 76% helix, 0% strand | P00127 |
| G, R | Cytochrome B-C1 complex subunit 7 | protein | 126 | 67% helix, 2% strand | P00128 |
| H, S | Cytochrome B-C1 complex subunit 8 | protein | 93 | 54% helix, 8% strand | P08525 |
| I, T | Cytochrome B-C1 complex subunit 9 | protein | 57 | 84% helix, 0% strand | P22289 |
| J, U | Cytochrome B-C1 complex subunit 10 | protein | 76 | 50% helix, 8% strand | P37299 |
| a, m | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 534 | 68% helix, 1% strand | P00401 |
| b, n | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 236 | 31% helix, 25% strand | P00410 |
| c, o | Cytochrome C oxidase subunit 3 (EC 1.9.3.1) | protein | 269 | 72% helix, 0% strand | P00420 |
| d, p | Cytochrome C oxidase subunit 4, mitochondrial (EC 1.9.3.1) | protein | 121 | 13% helix, 17% strand | P04037 |
| e, q | Cytochrome C oxidase polypeptide 5A, mitochondrial (EC 1.9.3.1) | protein | 133 | 59% helix, 0% strand | P00424 |
| f, r | Cytochrome C oxidase subunit 6, mitochondrial (EC 1.9.3.1) | protein | 102 | 70% helix, 1% strand | P00427 |
| g, s | Cytochrome C oxidase subunit 7 (EC 1.9.3.1) | protein | 59 | 61% helix, 0% strand | P10174 |
| h, t | Cytochrome C oxidase polypeptide VIII, mitochondrial (EC 1.9.3.1) | protein | 47 | 53% helix, 0% strand | P04039 |
| i, u | Cytochrome C oxidase subunit 7A (EC 1.9.3.1) | protein | 55 | 85% helix, 2% strand | P07255 |
| j, v | Cytochrome C oxidase subunit 6B (EC 1.9.3.1) | protein | 77 | 57% helix, 0% strand | Q01519 |
| k, w | Cytochrome C oxidase subunit 6A, mitochondrial (EC 1.9.3.1) | protein | 113 | 51% helix, 0% strand | P32799 |
| l, x | COX26 | protein | 45 | 76% helix, 0% strand | Q2V2P9 |
Ligands and binding sites
- PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · 28 copies · chains A, C, D, E, N, J, I, G, H, L, O, P, U, R, S, a, b, i, e, l, c, d, k, h, m, n, u, o, q, x, p, w, t
- CDL · Cardiolipin · ligand · 8 copies · chains A, C, I, J, D, E, H, e, G, L, N, T, U, O, R, S, P, q
- PCF · 1,2-diacyl-sn-glycero-3-phoshocholine · ligand · 8 copies · chains C, G, H, e, A, E, I, N, R, S, P, q, L, T, U, a, m
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, N
- HEA · Heme-A · ligand · 4 copies · chains a, b, m, n
- HEC · Heme C · ligand · 2 copies · chains D, O
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, P
- UQ6 · 5-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18, 22-hexaenyl)-2,3-dimethoxy-6-methyl-benzene-1,4-diol · ligand · chains C, N
- CUA · Dinuclear copper ion · metal · 4 copies · chains b, n
- CU · Copper (II) ion · metal · 2 copies · chains a, m
- CA · Calcium ion · metal · 2 copies · chains a, m
- MG · Magnesium ion · metal · 2 copies · chains a, b, m, n
- ZN · Zinc ion · metal · 2 copies · chains d, p
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 | 985 | 0.91 | 0.93 | 98 | HEA |
| 2 | 1025 | 0.91 | 0.93 | 108 | HEA |
| 3 | 1038 | 0.85 | 0.86 | 100 | PEF |
| 4 | 1089 | 0.85 | 0.85 | 103 | PEF |
| 5 | 629 | 0.83 | 0.87 | 63 | HEM |
Interfaces
154 interfaces between chains.
- m–n · 3674 Ų buried · 29 hydrogen bonds · protein-protein
- a–b · 3644 Ų buried · 29 hydrogen bonds · protein-protein
- a–c · 2549 Ų buried · 17 hydrogen bonds · protein-protein
- m–o · 2525 Ų buried · 16 hydrogen bonds · protein-protein
- C–G · 2007 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 cofactor, 1 covalent (disulfide, heme c attachment, covalent ligand).
Compared structures
- 6HU9 · III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae · the same entry in another collection · chain L against L, 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 P37299
- Every structure of UniProt P00401
- Every structure of UniProt P00410
- Every structure of UniProt P00420
- Every structure of UniProt P04037
- Every structure of UniProt P00424
- Every structure of UniProt P00427
- Every structure of UniProt P10174
- Every structure of UniProt P04039
- Every structure of UniProt P07255
- Every structure of UniProt Q01519
- Every structure of UniProt P32799
- Every structure of UniProt Q2V2P9
- Elsewhere: RCSB PDB 6HU9 · PDBe 6HU9 · UniProt P07256 · UniProt P07257 · UniProt P00163 · UniProt P07143 · UniProt P08067 · UniProt P00127 · UniProt P00128 · UniProt P08525 · UniProt P22289 · UniProt P37299 · UniProt P00401 · UniProt P00410 · UniProt P00420 · UniProt P04037 · UniProt P00424 · UniProt P00427 · UniProt P10174 · UniProt P04039 · UniProt P07255 · UniProt Q01519 · UniProt P32799 · UniProt Q2V2P9
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