MolNFT v1 · #13089 · protein
Quinol-fumarate reductase with menaquinol molecules
1L0V · Fumarate reductase flavoprotein subunit: “Quinol-fumarate reductase with menaquinol molecules”. X-ray diffraction, 7 ligands (MQ7, CE1, OAA), 20 pockets (best druggability 0.87). MolNFT v1 #13089 on GenesisL1: 3D structure, binding…
- PDB
- 1L0V
- Type
- protein
- Length
- 2,138 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate reductase flavoprotein subunit; Fumarate reductase iron-sulfur protein; Fumarate…
- EC
- 1.3.99.1
- UniProt
- P00363, P0AC47, P0A8Q0, P0A8Q3
- Ligands
- MQ7, CE1, OAA, FES, F3S, SF4, FAD
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M | Fumarate reductase flavoprotein subunit (EC 1.3.99.1) | protein | 577 | 38% helix, 19% strand | P00363 |
| B, N | Fumarate reductase iron-sulfur protein (EC 1.3.99.1) | protein | 243 | 40% helix, 16% strand | P0AC47 |
| C, O | Fumarate reductase 15 kda hydrophobic protein | protein | 130 | 74% helix, 2% strand | P0A8Q0 |
| D, P | Fumarate reductase 13 kda hydrophobic protein | protein | 119 | 74% helix, 0% strand | P0A8Q3 |
Ligands and binding sites
- MQ7 · Menaquinone-7 · ligand · 4 copies · chains C, D, B, O, P, N
- CE1 · O-dodecanyl octaethylene glycol · ligand · 4 copies · chains B, D, P, N, O
- OAA · Oxaloacetate ion · 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
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.87 | 0.95 | 65 | OAA, FAD |
| 2 | 675 | 0.83 | 0.87 | 84 | OAA, FAD |
| 3 | 749 | 0.81 | 0.84 | 66 | empty |
| 4 | 772 | 0.79 | 0.83 | 63 | empty |
| 5 | 261 | 0.78 | 0.90 | 25 | MQ7 |
Interfaces
13 interfaces between chains.
- M–N · 2777 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2660 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2372 Ų buried · 13 hydrogen bonds · protein-protein
- O–P · 2290 Ų buried · 13 hydrogen bonds · protein-protein
- N–O · 1477 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 1L0V · Quinol-Fumarate Reductase with Menaquinol Molecules · 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 1L0V · PDBe 1L0V · UniProt P00363 · UniProt P0AC47 · UniProt P0A8Q0 · UniProt P0A8Q3
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