Research workbench
Assembly intermediate of the plant mitochondrial complex I
Analyse Assembly intermediate of the plant mitochondrial complex I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A24
- Type
- protein
- Length
- 6,253 residues
- Chains
- 34
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 51KDA; NAD2M; NAD3M; NAD6M; NAD1M; NAD4LM; Pgiv; B16.6; Mwfe; B9; B14.5A; B14.5B; 15KDA…
- Ligands
- SF4, T7X, FES, FMN, CDL, PEV, NDP, BCT, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 34 distinct chains · 40% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 51KDA | protein | 429 | 43% helix, 10% strand | — |
| I | NAD2M | protein | 481 | 76% helix, 1% strand | — |
| J | NAD3M | protein | 96 | 73% helix, 0% strand | — |
| N | NAD6M | protein | 149 | 58% helix, 0% strand | — |
| H | NAD1M | protein | 318 | 59% helix, 0% strand | — |
| K | NAD4LM | protein | 85 | 86% helix, 0% strand | — |
| Y | Pgiv | protein | 98 | 76% helix, 0% strand | — |
| Z | B16.6 | protein | 140 | 44% helix, 1% strand | — |
| V | Mwfe | protein | 57 | 70% helix, 0% strand | — |
| W | B9 | protein | 37 | 68% helix, 0% strand | — |
| S | B14.5A | protein | 101 | 13% helix, 9% strand | — |
| i | B14.5B | protein | 63 | 68% helix, 0% strand | — |
| j | 15KDA | protein | 68 | 71% helix, 0% strand | — |
| G | NAD7M | protein | 382 | 45% helix, 9% strand | — |
| C | 75KDA | protein | 693 | 25% helix, 14% strand | — |
| T | 39KDA | protein | 328 | 32% helix, 11% strand | — |
| F | NAD9M | protein | 178 | 12% helix, 18% strand | — |
| B | 24KDA | protein | 219 | 34% helix, 8% strand | — |
| O | 18KDA | protein | 111 | 14% helix, 15% strand | — |
| P | 13KDA | protein | 71 | 14% helix, 15% strand | — |
| R | B13 | protein | 121 | 51% helix, 4% strand | — |
| U | B17.2 | protein | 122 | 11% helix, 12% strand | — |
| E | Psst | protein | 153 | 41% helix, 10% strand | — |
| D | Tyky | protein | 177 | 37% helix, 16% strand | — |
| X | B14 | protein | 103 | 66% helix, 0% strand | — |
| c | Mnll | protein | 99 | 52% helix, 0% strand | — |
| Q | B8 | protein | 92 | 33% helix, 18% strand | — |
| k | ACPM1 | protein | 78 | 47% helix, 3% strand | — |
| r | UNK1 | protein | 24 | 0% helix, 13% strand | — |
| n | P2 | protein | 27 | 74% helix, 0% strand | — |
| o | CAL1 | protein | 202 | 16% helix, 20% strand | — |
| q | CA1 | protein | 228 | 20% helix, 15% strand | — |
| p | CA1 | protein | 224 | 21% helix, 18% strand | — |
| z | Gldh | protein | 499 | 30% helix, 17% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, G, C, E, D
- T7X · Phosphatidylinositol · ligand · 2 copies · chains I, i, c, n, q, p
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains C, A, B
- FMN · Flavin mononucleotide · ligand · chains A
- CDL · Cardiolipin · ligand · chains I, i, c, n, q, p
- PEV · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains H, W, G, D
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains T
- BCT · Bicarbonate ion · ligand · chains q, p
- ZN · Zinc ion · metal · 2 copies · chains P, q, 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 | 1002 | 0.87 | 0.88 | 107 | NDP |
| 2 | 1077 | 0.87 | 0.88 | 135 | empty |
| 3 | 959 | 0.86 | 0.87 | 90 | empty |
| 4 | 739 | 0.85 | 0.88 | 59 | empty |
| 5 | 206 | 0.83 | 0.97 | 36 | empty |
Interfaces
122 interfaces between chains.
- A–B · 3111 Ų buried · 41 hydrogen bonds · protein-protein
- q–p · 2973 Ų buried · 29 hydrogen bonds · protein-protein
- o–p · 2674 Ų buried · 32 hydrogen bonds · protein-protein
- J–H · 2530 Ų buried · 9 hydrogen bonds · protein-protein
- C–O · 2311 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7A24 · Assembly intermediate of the plant mitochondrial complex I · the same entry in another collection · chain F against F, 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
- Elsewhere: RCSB PDB 7A24 · PDBe 7A24
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