MolNFT v1 · #164515 · protein
The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae
6T0B · Cytochrome B-C1 complex subunit 1, mitochondrial: “The III2-IV(5B)2 respiratory supercomplex from S. cerevisiae”. Electron microscopy, 12 ligands (PEF, CDL, PCF), 20 pockets (best druggability 0.91). MolNFT v1 #164515 on GenesisL1…
- PDB
- 6T0B
- Type
- protein
- Length
- 7,837 residues
- Chains
- 46
- 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, 1.9.3.1
- UniProt
- P07256, P07257, P00163, P07143, P08067, P00127, P00128, P08525, P22289, P37299, P00401, P00410, P00420, P04037, P00425, P00427, P10174, P04039, P07255, Q01519, P32799, Q2V2P9, P53721
- Ligands
- PEF, CDL, PCF, HEM, HEA, HEC, FES, CUA, CU, CA, MG, ZN
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 25 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 431 | 43% helix, 18% strand | P07256 |
| B, M | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 352 | 39% helix, 22% strand | P07257 |
| C, N | Cytochrome B | protein | 385 | 68% helix, 3% strand | P00163 |
| D, O | Cytochrome C1, heme protein, mitochondrial | protein | 247 | 39% helix, 10% strand | P07143 |
| E, P | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 7.1.1.8) | protein | 185 | 28% helix, 15% strand | P08067 |
| F, Q | Cytochrome B-C1 complex subunit 6 | protein | 75 | 64% helix, 0% strand | P00127 |
| G, R | Cytochrome B-C1 complex subunit 7 | protein | 126 | 65% helix, 2% strand | P00128 |
| H, S | Cytochrome B-C1 complex subunit 8 | protein | 93 | 53% 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 | 41% helix, 5% strand | P37299 |
| a, n | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 534 | 68% helix, 1% strand | P00401 |
| b, o | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 236 | 31% helix, 26% strand | P00410 |
| c, p | Cytochrome C oxidase subunit 3 (EC 1.9.3.1) | protein | 269 | 71% helix, 0% strand | P00420 |
| d | Cytochrome C oxidase subunit 4, mitochondrial (EC 1.9.3.1) | protein | 120 | 16% helix, 18% strand | P04037 |
| e, r | Cytochrome C oxidase polypeptide 5B, mitochondrial (EC 1.9.3.1) | protein | 133 | 53% helix, 0% strand | P00425 |
| f, s | Cytochrome C oxidase subunit 6, mitochondrial (EC 1.9.3.1) | protein | 102 | 71% helix, 1% strand | P00427 |
| g, t | Cytochrome C oxidase subunit 7 (EC 1.9.3.1) | protein | 59 | 66% helix, 0% strand | P10174 |
| h, u | Cytochrome C oxidase polypeptide VIII, mitochondrial (EC 1.9.3.1) | protein | 51 | 49% helix, 0% strand | P04039 |
| i, v | Cytochrome C oxidase subunit 7A (EC 1.9.3.1) | protein | 55 | 84% helix, 2% strand | P07255 |
| j | Cytochrome C oxidase subunit 6B (EC 1.9.3.1) | protein | 75 | 48% helix, 4% strand | Q01519 |
| k, x | Cytochrome C oxidase subunit 6A, mitochondrial (EC 1.9.3.1) | protein | 113 | 51% helix, 1% strand | P32799 |
| l, y | COX26 | protein | 45 | 69% helix, 0% strand | Q2V2P9 |
| m, z | Respiratory supercomplex factor 2, mitochondrial | protein | 99 | 69% helix, 0% strand | P53721 |
| q | Cytochrome C oxidase subunit 4, mitochondrial (EC 1.9.3.1) | protein | 121 | 9% helix, 16% strand | P04037 |
| w | Cytochrome C oxidase subunit 6B (EC 1.9.3.1) | protein | 75 | 52% helix, 1% strand | Q01519 |
Ligands and binding sites
- PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · 26 copies · chains A, C, D, E, N, I, a, e, h, H, G, J, L, O, P, T, R, S, c, b, i, l, k, n, o, s, v, r, y, p
- CDL · Cardiolipin · ligand · 8 copies · chains A, C, I, J, G, H, D, E, e, L, N, U, R, S, O, P, T, r
- PCF · 1,2-diacyl-sn-glycero-3-phoshocholine · ligand · 7 copies · chains C, G, H, e, A, E, I, N, R, S, L, P, T, U, a, n, r
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, N
- HEA · Heme-A · ligand · 4 copies · chains a, b, n, o
- HEC · Heme C · ligand · 2 copies · chains D, O
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, P
- CUA · Dinuclear copper ion · ligand · 2 copies · chains b, o
- CU · Copper (II) ion · metal · 2 copies · chains a, n
- CA · Calcium ion · metal · 2 copies · chains a, n
- MG · Magnesium ion · metal · 2 copies · chains a, b, n, o
- ZN · Zinc ion · metal · 2 copies · chains d, q
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 | 1083 | 0.91 | 0.92 | 106 | HEA, MG |
| 2 | 1045 | 0.91 | 0.92 | 100 | HEA, MG |
| 3 | 658 | 0.83 | 0.87 | 66 | HEM |
| 4 | 734 | 0.83 | 0.86 | 77 | PEF |
| 5 | 678 | 0.82 | 0.86 | 66 | HEM |
Interfaces
155 interfaces between chains.
- n–o · 3641 Ų buried · 31 hydrogen bonds · protein-protein
- a–b · 3590 Ų buried · 32 hydrogen bonds · protein-protein
- n–p · 2580 Ų buried · 16 hydrogen bonds · protein-protein
- a–c · 2445 Ų buried · 18 hydrogen bonds · protein-protein
- C–G · 1973 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 cofactor, 1 covalent (disulfide, heme c attachment, covalent ligand).
Compared structures
- 6T0B · The III2-IV(5B)2 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 P00425
- 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
- Every structure of UniProt P53721
- Elsewhere: RCSB PDB 6T0B · PDBe 6T0B · 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 P00425 · UniProt P00427 · UniProt P10174 · UniProt P04039 · UniProt P07255 · UniProt Q01519 · UniProt P32799 · UniProt Q2V2P9 · UniProt P53721
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