Research workbench
Respiratory complex I from escherichia COLI - conformation 3
Analyse Respiratory complex I from escherichia COLI - conformation 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NYV
- Type
- protein
- Length
- 4,618 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-quinone oxidoreductase subunit B; NADH-quinone oxidoreductase subunit C/D…
- EC
- 7.1.1.-, 7.1.1.2, 1.6.5.11, 1.6.5.3, 1.6.99.5
- UniProt
- P0AFC7, P33599, P0AFD1, P31979, P33602, P0AFD6, P0AFE4, P0AFE0, P0AFC3, P0AFD4, P0AFE8, A0A1V3W1N5, P0AFF0
- Ligands
- SF4, FES, FMN, CA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 13 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | NADH-quinone oxidoreductase subunit B (EC 7.1.1.-) | protein | 159 | 38% helix, 13% strand | P0AFC7 |
| D | NADH-quinone oxidoreductase subunit C/D (EC 7.1.1.2) | protein | 588 | 39% helix, 15% strand | P33599 |
| E | NADH-quinone oxidoreductase subunit E (EC 7.1.1.2) | protein | 156 | 52% helix, 12% strand | P0AFD1 |
| F | NADH-quinone oxidoreductase subunit F (EC 7.1.1.2) | protein | 441 | 42% helix, 13% strand | P31979 |
| G | NADH-quinone oxidoreductase subunit G (EC 7.1.1.2) | protein | 907 | 31% helix, 19% strand | P33602 |
| I | NADH-quinone oxidoreductase subunit I (EC 7.1.1.2) | protein | 158 | 15% helix, 22% strand | P0AFD6 |
| K | NADH-quinone oxidoreductase subunit K (EC 7.1.1.-) | protein | 100 | 74% helix, 3% strand | P0AFE4 |
| J | NADH-quinone oxidoreductase subunit J (EC 7.1.1.-) | protein | 164 | 75% helix, 2% strand | P0AFE0 |
| A | NADH-quinone oxidoreductase subunit a (EC 7.1.1.-) | protein | 92 | 71% helix, 0% strand | P0AFC3 |
| H | NADH-quinone oxidoreductase subunit H (EC 7.1.1.-) | protein | 270 | 63% helix, 0% strand | P0AFD4 |
| M | NADH-quinone oxidoreductase subunit M (EC 7.1.1.-) | protein | 504 | 70% helix, 2% strand | P0AFE8 |
| L | NADH-quinone oxidoreductase subunit L (EC 1.6.5.11, 1.6.5.3, 1.6.99.5) | protein | 612 | 71% helix, 4% strand | A0A1V3W1N5 |
| N | NADH-quinone oxidoreductase subunit N (EC 7.1.1.-) | protein | 467 | 73% helix, 1% strand | P0AFF0 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 7 copies · chains B, D, F, G, I
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, G
- FMN · Flavin mononucleotide · ligand · chains F
- CA · Calcium ion · metal · chains G
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 | 1194 | 0.83 | 0.84 | 83 | empty |
| 2 | 1176 | 0.82 | 0.83 | 158 | empty |
| 3 | 1029 | 0.81 | 0.82 | 93 | empty |
| 4 | 570 | 0.80 | 0.86 | 69 | empty |
| 5 | 139 | 0.79 | 0.97 | 36 | empty |
Interfaces
30 interfaces between chains.
- K–J · 3127 Ų buried · 13 hydrogen bonds · protein-protein
- M–L · 2670 Ų buried · 22 hydrogen bonds · protein-protein
- B–I · 2017 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 2010 Ų buried · 25 hydrogen bonds · protein-protein
- G–I · 1947 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 3 modified (covalent ligand, oxidation).
Compared structures
- 7NYV · Respiratory complex I from Escherichia coli - conformation 3 · the same entry in another collection · chain J against J, 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 P0AFC7
- Every structure of UniProt P33599
- Every structure of UniProt P0AFD1
- Every structure of UniProt P31979
- Every structure of UniProt P33602
- Every structure of UniProt P0AFD6
- Every structure of UniProt P0AFE4
- Every structure of UniProt P0AFE0
- Every structure of UniProt P0AFC3
- Every structure of UniProt P0AFD4
- Every structure of UniProt P0AFE8
- Every structure of UniProt A0A1V3W1N5
- Every structure of UniProt P0AFF0
- Elsewhere: RCSB PDB 7NYV · PDBe 7NYV · UniProt P0AFC7 · UniProt P33599 · UniProt P0AFD1 · UniProt P31979 · UniProt P33602 · UniProt P0AFD6 · UniProt P0AFE4 · UniProt P0AFE0 · UniProt P0AFC3 · UniProt P0AFD4 · UniProt P0AFE8 · UniProt A0A1V3W1N5 · UniProt P0AFF0
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