Research workbench
Crystal structure of the membrane domain of respiratory complex I from E. COLI at 3.0 ångström resolution
Analyse Crystal structure of the membrane domain of respiratory complex I from E. COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RKO
- Type
- protein
- Length
- 3,904 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-quinone oxidoreductase subunit L; NADH-quinone oxidoreductase subunit M…
- EC
- 1.6.5.3
- UniProt
- C6E9S4, C6E9S5, C6E9S6, C6E9S3, C6E9R4, C6E9S2
- Ligands
- LFA, CA7
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 74% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B | NADH-quinone oxidoreductase subunit L (EC 1.6.5.3) | protein | 612 | 73% helix, 4% strand | C6E9S4 |
| M, C | NADH-quinone oxidoreductase subunit M (EC 1.6.5.3) | protein | 504 | 73% helix, 4% strand | C6E9S5 |
| N, D | NADH-quinone oxidoreductase subunit N (EC 1.6.5.3) | protein | 473 | 74% helix, 1% strand | C6E9S6 |
| K, G | NADH-quinone oxidoreductase subunit K (EC 1.6.5.3) | protein | 100 | 75% helix, 2% strand | C6E9S3 |
| A, E | NADH-quinone oxidoreductase subunit a (EC 1.6.5.3) | protein | 95 | 82% helix, 0% strand | C6E9R4 |
| J, F | NADH-quinone oxidoreductase subunit J (EC 1.6.5.3) | protein | 168 | 73% helix, 0% strand | C6E9S2 |
Ligands and binding sites
- LFA · Eicosane · ligand · 18 copies · chains L, M, N, B, C, D
- CA7 · 7-cyclohexylheptyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside · ligand · 2 copies · chains L, M, B, C
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 | 663 | 0.78 | 0.82 | 47 | LFA |
| 2 | 729 | 0.78 | 0.82 | 59 | LFA |
| 3 | 1019 | 0.77 | 0.79 | 91 | empty |
| 4 | 618 | 0.73 | 0.79 | 48 | empty |
| 5 | 545 | 0.72 | 0.79 | 48 | empty |
Interfaces
28 interfaces between chains.
- G–F · 3583 Ų buried · 22 hydrogen bonds · protein-protein
- K–J · 3569 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2440 Ų buried · 17 hydrogen bonds · protein-protein
- L–M · 2435 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 2297 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3RKO · Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0… · 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 C6E9S4
- Every structure of UniProt C6E9S5
- Every structure of UniProt C6E9S6
- Every structure of UniProt C6E9S3
- Every structure of UniProt C6E9R4
- Every structure of UniProt C6E9S2
- Elsewhere: RCSB PDB 3RKO · PDBe 3RKO · UniProt C6E9S4 · UniProt C6E9S5 · UniProt C6E9S6 · UniProt C6E9S3 · UniProt C6E9R4 · UniProt C6E9S2
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