Research workbench
E. COLI quinol-fumarate reductase with bound inhibitor hqno
Analyse E. COLI quinol-fumarate reductase with bound inhibitor hqno in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KF6
- Type
- protein
- Length
- 2,138 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate reductase flavoprotein; Fumarate reductase iron-sulfur protein; Fumarate…
- EC
- 1.3.99.1
- UniProt
- P00363, P0AC47, P0A8Q0, P0A8Q3
- Ligands
- CE1, OAA, FAD, FES, F3S, SF4, HQO, K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M | Fumarate reductase flavoprotein (EC 1.3.99.1) | protein | 577 | 39% helix, 19% strand | P00363 |
| B, N | Fumarate reductase iron-sulfur protein (EC 1.3.99.1) | protein | 243 | 40% helix, 15% strand | P0AC47 |
| C, O | Fumarate reductase 15 kda hydrophobic protein | protein | 130 | 73% helix, 2% strand | P0A8Q0 |
| D, P | Fumarate reductase 13 kda hydrophobic protein | protein | 119 | 73% helix, 0% strand | P0A8Q3 |
Ligands and binding sites
- CE1 · O-dodecanyl octaethylene glycol · ligand · 5 copies · chains O, P, B, D, N
- OAA · Oxaloacetate ion · ligand · 2 copies · chains A, M
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, M
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, N
- F3S · FE3-S4 cluster · ligand · 2 copies · chains B, N
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, N
- HQO · 2-heptyl-4-hydroxy quinoline N-oxide · ligand · 2 copies · chains B, C, D, N, O, P
- K · Potassium ion · metal · 2 copies · chains A, M
- ACT · Acetate ion · additive · 3 copies · chains A, B, M, N
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.85 | 0.90 | 90 | OAA, FAD |
| 2 | 1020 | 0.84 | 0.85 | 121 | OAA, FAD, 1PE |
| 3 | 753 | 0.80 | 0.83 | 58 | ACT |
| 4 | 229 | 0.77 | 0.90 | 25 | empty |
| 5 | 239 | 0.76 | 0.89 | 25 | empty |
Interfaces
13 interfaces between chains.
- M–N · 2701 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2667 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2377 Ų buried · 13 hydrogen bonds · protein-protein
- O–P · 2262 Ų buried · 13 hydrogen bonds · protein-protein
- N–O · 1505 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 1KF6 · E. coli Quinol-Fumarate Reductase with Bound Inhibitor HQNO · the same entry in another collection · chain P against P, TM-score 1.00
- P00363 · AlphaFold monomer V2.0 prediction for fumarate reductase flavoprotein subunit (P00363) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0AC47 · AlphaFold monomer V2.0 prediction for fumarate reductase iron-sulfur subunit (P0AC47) · a predicted model of the same protein · chain N against A, TM-score 0.99
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 P00363
- Every structure of UniProt P0AC47
- Every structure of UniProt P0A8Q0
- Every structure of UniProt P0A8Q3
- Elsewhere: RCSB PDB 1KF6 · PDBe 1KF6 · UniProt P00363 · UniProt P0AC47 · UniProt P0A8Q0 · UniProt P0A8Q3
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