MolNFT v1 · #126159 · protein
Cryo-EM of bovine respirasome
5LUF · Cytochrome B-C1 complex subunit 1, mitochondrial: “Cryo-EM of bovine respirasome”. Electron microscopy, 8 ligands (SF4, HEM, FES), 20 pockets (best druggability 0.92). MolNFT v1 #126159 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5LUF
- Type
- protein
- Length
- 11,468 residues
- Chains
- 62
- 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
- P31800, P23004, P00157, P00125, P13272, P00129, P13271, P00126, P00130, P07552, P00396, P68530, P00415, P00423, P00426, P00428, P07471, P00429, P04038, P07470, P13183, P00430, P10175
- Ligands
- SF4, HEM, FES, HEC, HEA, CU, MG, ZN
- Pockets
- 20 · best druggability 0.92
Structure
electron microscopy · 50 distinct chains · 57% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| c, l | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 446 | 46% helix, 16% strand | P31800 |
| m, n | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 419 | 46% helix, 16% strand | P23004 |
| b, o | Cytochrome B | protein | 379 | 69% helix, 2% strand | P00157 |
| d, p | Cytochrome C1, heme protein, mitochondrial | protein | 241 | 41% helix, 3% strand | P00125 |
| e | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 75 | 59% helix, 1% strand | P13272 |
| f, r | Cytochrome B-C1 complex subunit 7 | protein | 106 | 67% helix, 0% strand | P00129 |
| g, s | Cytochrome B-C1 complex subunit 8 | protein | 81 | 57% helix, 9% strand | P13271 |
| h, t | Cytochrome B-C1 complex subunit 6, mitochondrial | protein | 64 | 78% helix, 0% strand | P00126 |
| i, u | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 33 | 0% helix, 21% strand | P13272 |
| j, v | Cytochrome B-C1 complex subunit 9 | protein | 62 | 69% helix, 0% strand | P00130 |
| k, w | Cytochrome B-C1 complex subunit 10 | protein | 22 | 86% helix, 0% strand | P07552 |
| q | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 196 | 32% helix, 18% strand | P13272 |
| x | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 514 | 71% helix, 2% strand | P00396 |
| y | Cytochrome C oxidase subunit 2 | protein | 227 | 33% helix, 26% strand | P68530 |
| z | Cytochrome C oxidase subunit 3 | protein | 261 | 76% helix, 1% strand | P00415 |
| 1 | Cytochrome C oxidase subunit 4 isoform 1, mitochondrial | protein | 144 | 54% helix, 4% strand | P00423 |
| 2 | Cytochrome C oxidase subunit 5A, mitochondrial | protein | 109 | 65% helix, 1% strand | P00426 |
| 3 | Cytochrome C oxidase subunit 5B, mitochondrial | protein | 98 | 15% helix, 30% strand | P00428 |
| 4 | Cytochrome C oxidase subunit 6A2, mitochondrial | protein | 84 | 30% helix, 0% strand | P07471 |
| 5 | Cytochrome C oxidase subunit 6B1 | protein | 75 | 56% helix, 1% strand | P00429 |
| 6 | Cytochrome C oxidase subunit 6C | protein | 73 | 71% helix, 1% strand | P04038 |
| 7 | Cytochrome C oxidase subunit 7A1, mitochondrial | protein | 56 | 68% helix, 0% strand | P07470 |
| 8 | Cytochrome C oxidase subunit 7B, mitochondrial | protein | 49 | 55% helix, 0% strand | P13183 |
| 9 | Cytochrome C oxidase subunit 7C, mitochondrial | protein | 47 | 57% helix, 0% strand | P00430 |
| 0 | Cytochrome C oxidase subunit 8B, mitochondrial | protein | 43 | 67% helix, 5% strand | P10175 |
| A | Complex I | protein | 83 | 83% helix, 0% strand | — |
| B | Complex I | protein | 143 | 38% helix, 10% strand | — |
| C | Complex I | protein | 154 | 23% helix, 24% strand | — |
| D | Complex I | protein | 384 | 46% helix, 10% strand | — |
| E | Complex I | protein | 159 | 45% helix, 9% strand | — |
| F | Complex I | protein | 411 | 49% helix, 11% strand | — |
| G | Complex I | protein | 527 | 31% helix, 12% strand | — |
| H | Complex I | protein | 285 | 73% helix, 0% strand | — |
| I | Complex I | protein | 162 | 35% helix, 13% strand | — |
| J | Complex I | protein | 131 | 82% helix, 0% strand | — |
| K | Complex I | protein | 84 | 81% helix, 0% strand | — |
| L | Complex I | protein | 558 | 73% helix, 2% strand | — |
| M | Complex I | protein | 439 | 72% helix, 0% strand | — |
| N | Complex I | protein | 326 | 79% helix, 0% strand | — |
| O | Complex I | protein | 181 | 55% helix, 5% strand | — |
| P | Complex I | protein | 252 | 39% helix, 15% strand | — |
| Q | Complex I | protein | 69 | 16% helix, 25% strand | — |
| R | Complex I | protein | 47 | 0% helix, 40% strand | — |
| S | Complex I | protein | 80 | 35% helix, 24% strand | — |
| T, V, a | Complex I | protein | 71 | 63% helix, 3% strand | — |
| W | Complex I | protein | 72 | 76% helix, 0% strand | — |
| X | Complex I | protein | 329 | 77% helix, 1% strand | — |
| Y | Complex I | protein | 106 | 79% helix, 0% strand | — |
| U | Complex I | protein | 250 | 84% helix, 0% strand | — |
| Z | Complex I | protein | 266 | 71% helix, 1% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains B, F, G, I
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains b, o
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains q, E, F, G
- HEC · Heme C · ligand · 2 copies · chains d, p
- HEA · Heme-A · ligand · 2 copies · chains x, y
- CU · Copper (II) ion · metal · 3 copies · chains x, y
- MG · Magnesium ion · metal · chains x, y
- ZN · Zinc ion · metal · chains 3
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 | 1056 | 0.92 | 0.94 | 120 | MG, HEA |
| 2 | 527 | 0.87 | 0.93 | 62 | HEM |
| 3 | 528 | 0.87 | 0.93 | 64 | HEM |
| 4 | 1031 | 0.85 | 0.86 | 180 | empty |
| 5 | 974 | 0.85 | 0.86 | 85 | empty |
Interfaces
154 interfaces between chains.
- x–y · 3545 Ų buried · 33 hydrogen bonds · protein-protein
- x–z · 2701 Ų buried · 21 hydrogen bonds · protein-protein
- l–n · 2102 Ų buried · 31 hydrogen bonds · protein-protein
- c–m · 2096 Ų buried · 30 hydrogen bonds · protein-protein
- x–9 · 1764 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 cofactor (disulfide, heme c attachment).
Compared structures
- 5LUF · Cryo-EM of bovine respirasome · the same entry in another collection · chain i against i, 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 P31800
- Every structure of UniProt P23004
- Every structure of UniProt P00157
- Every structure of UniProt P00125
- Every structure of UniProt P13272
- Every structure of UniProt P00129
- Every structure of UniProt P13271
- Every structure of UniProt P00126
- Every structure of UniProt P00130
- Every structure of UniProt P07552
- Every structure of UniProt P00396
- Every structure of UniProt P68530
- Every structure of UniProt P00415
- Every structure of UniProt P00423
- Every structure of UniProt P00426
- Every structure of UniProt P00428
- Every structure of UniProt P07471
- Every structure of UniProt P00429
- Every structure of UniProt P04038
- Every structure of UniProt P07470
- Every structure of UniProt P13183
- Every structure of UniProt P00430
- Every structure of UniProt P10175
- Elsewhere: RCSB PDB 5LUF · PDBe 5LUF · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130 · UniProt P07552 · UniProt P00396 · UniProt P68530 · UniProt P00415 · UniProt P00423 · UniProt P00426 · UniProt P00428 · UniProt P07471 · UniProt P00429 · UniProt P04038 · UniProt P07470 · UniProt P13183 · UniProt P00430 · UniProt P10175
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.