MolNFT v1 · #170913 · protein
CIII2/CIV respiratory supercomplex from saccharomyces cerevisiae
6YMX · Cytochrome C oxidase subunit 1: “CIII2/CIV respiratory supercomplex from saccharomyces cerevisiae”. Electron microscopy, 15 ligands (PTY, HEM, PCF), 20 pockets (best druggability 0.91). MolNFT v1 #170913 on GenesisL1: 3D structure…
- PDB
- 6YMX
- Type
- protein
- Length
- 5,759 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 1; Cytochrome C oxidase subunit 2; Cytochrome C oxidase…
- EC
- 1.9.3.1, 7.1.1.8
- UniProt
- P00401, P00410, P00420, P04037, P00424, P00427, P10174, P04039, P07255, Q01519, P32799, Q2V2P9, P07256, P07257, P00163, P07143, P08067, P00127, P00128, P08525, P22289, P37299
- Ligands
- PTY, HEM, PCF, HEA, CN3, 6PH, 8PE, UQ6, 9PE, 7PH, FES, CUA, CN5, CU, ZN
- Pockets
- 20 · best druggability 0.91
Structure
electron microscopy · 25 distinct chains · 44% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 530 | 53% helix, 0% strand | P00401 |
| b | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 236 | 25% helix, 17% strand | P00410 |
| c | Cytochrome C oxidase subunit 3 (EC 1.9.3.1) | protein | 268 | 54% helix, 0% strand | P00420 |
| d | Cytochrome C oxidase subunit 4, mitochondrial | protein | 117 | 10% helix, 7% strand | P04037 |
| e | Cytochrome C oxidase subunit 5A, mitochondrial | protein | 128 | 46% helix, 0% strand | P00424 |
| f | Cytochrome C oxidase subunit 6, mitochondrial | protein | 99 | 59% helix, 0% strand | P00427 |
| g | Cytochrome C oxidase subunit 7, mitochondrial | protein | 55 | 36% helix, 0% strand | P10174 |
| h | Cytochrome C oxidase subunit 8, mitochondrial | protein | 51 | 25% helix, 0% strand | P04039 |
| i | Cytochrome C oxidase subunit 9, mitochondrial | protein | 53 | 58% helix, 0% strand | P07255 |
| j | Cytochrome C oxidase subunit 12, mitochondrial | protein | 78 | 35% helix, 1% strand | Q01519 |
| k | Cytochrome C oxidase subunit 13, mitochondrial | protein | 114 | 36% helix, 0% strand | P32799 |
| m | Cytochrome C oxidase subunit 26, mitochondrial | protein | 38 | 66% helix, 0% strand | Q2V2P9 |
| A, L | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 431 | 39% helix, 18% strand | P07256 |
| B, M | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 352 | 34% helix, 20% strand | P07257 |
| C, N | Cytochrome B (EC 7.1.1.8) | protein | 385 | 60% helix, 2% strand | P00163 |
| D, O | Cytochrome C1, heme protein, mitochondrial (EC 7.1.1.8) | protein | 248 | 36% helix, 7% strand | P07143 |
| E, P | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 7.1.1.8) | protein | 185 | 23% helix, 17% strand | P08067 |
| F | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 74 | 58% helix, 0% strand | P00127 |
| G, R | Cytochrome B-C1 complex subunit 7, mitochondrial | protein | 126 | 58% helix, 2% strand | P00128 |
| H, S | Cytochrome B-C1 complex subunit 8, mitochondrial | protein | 93 | 40% helix, 10% strand | P08525 |
| I | Cytochrome B-C1 complex subunit 9, mitochondrial | protein | 54 | 76% helix, 0% strand | P22289 |
| Q | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 75 | 51% helix, 0% strand | P00127 |
| T | Cytochrome B-C1 complex subunit 9, mitochondrial | protein | 54 | 80% helix, 0% strand | P22289 |
| U | Cytochrome B-C1 complex subunit 10, mitochondrial | protein | 44 | 48% helix, 2% strand | P37299 |
| V | Cytochrome B-C1 complex subunit 10, mitochondrial | protein | 51 | 41% helix, 4% strand | P37299 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 7 copies · chains a, c, b, e, H, f, i, m, D, I
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains C, D, N, O
- PCF · 1,2-diacyl-sn-glycero-3-phoshocholine · ligand · 5 copies · chains a, c, k, e, I, b, m, A, E, L, P, T
- HEA · Heme-A · ligand · 2 copies · chains a, b
- CN3 · (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate · ligand · 2 copies · chains a, e, h, E, H, N, O, R, S
- 6PH · (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate · ligand · 2 copies · chains A, C, D, E, L, N, O, P
- 8PE · (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate · ligand · 2 copies · chains C, G, H, N, R, S
- 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 · 2 copies · chains C, N, P
- 9PE · (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate · ligand · 2 copies · chains C, N
- 7PH · (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate · ligand · 2 copies · chains C, D, E, N, O, P
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, P
- CUA · Dinuclear copper ion · ligand · chains b
- CN5 · (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10, 12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate · ligand · chains C, N
- CU · Copper (II) ion · metal · chains a
- ZN · Zinc ion · metal · chains d
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 | 1091 | 0.91 | 0.93 | 98 | CU, HEA |
| 2 | 405 | 0.85 | 0.93 | 42 | HEM |
| 3 | 819 | 0.84 | 0.86 | 77 | PTY |
| 4 | 652 | 0.82 | 0.87 | 63 | HEM |
| 5 | 450 | 0.82 | 0.89 | 58 | empty |
Interfaces
107 interfaces between chains.
- a–b · 3619 Ų buried · 14 hydrogen bonds · protein-protein
- a–c · 2540 Ų buried · 14 hydrogen bonds · protein-protein
- C–G · 1945 Ų buried · 10 hydrogen bonds · protein-protein
- N–R · 1937 Ų buried · 12 hydrogen bonds · protein-protein
- a–h · 1849 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6YMX · CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae · 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 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
- 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
- Elsewhere: RCSB PDB 6YMX · PDBe 6YMX · UniProt P00401 · UniProt P00410 · UniProt P00420 · UniProt P04037 · UniProt P00424 · UniProt P00427 · UniProt P10174 · UniProt P04039 · UniProt P07255 · UniProt Q01519 · UniProt P32799 · UniProt Q2V2P9 · UniProt P07256 · UniProt P07257 · UniProt P00163 · UniProt P07143 · UniProt P08067 · UniProt P00127 · UniProt P00128 · UniProt P08525 · UniProt P22289 · UniProt P37299
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