Research workbench
QUINOL:FUMARATE reductase from wolinella succinogenes
Analyse QUINOL:FUMARATE reductase from wolinella succinogenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E7P
- Type
- protein
- Length
- 4,592 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate reductase flavoprotein subunit; Fumarate reductase iron-sulfur subunit; Fumarate…
- EC
- 1.3.5.4, 1.3.5.1
- UniProt
- P17412, P17596, P17413
- Ligands
- HEM, FAD, FES, F3S, SF4, NA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Fumarate reductase flavoprotein subunit (EC 1.3.5.4) | protein | 655 | 35% helix, 16% strand | P17412 |
| B, E, H, K | Fumarate reductase iron-sulfur subunit (EC 1.3.5.1) | protein | 239 | 33% helix, 15% strand | P17596 |
| C, F, I, L | Fumarate reductase cytochrome B subunit | protein | 254 | 70% helix, 0% strand | P17413 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains B, C, E, F, H, I, K, L
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, D, G, J
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains B, E, H, K
- F3S · FE3-S4 cluster · ligand · 4 copies · chains B, E, H, K
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains B, E, H, K
- NA · Sodium ion · metal · 4 copies · chains A, D, G, J
- MLA · Malonic acid · additive · 4 copies · chains A, D, G, J
- LMT · Dodecyl-beta-D-maltoside · additive · 4 copies · chains C, F, I, L
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 | 719 | 0.89 | 0.93 | 75 | HEM |
| 2 | 700 | 0.89 | 0.93 | 70 | HEM |
| 3 | 705 | 0.89 | 0.93 | 74 | HEM |
| 4 | 693 | 0.89 | 0.93 | 71 | HEM |
| 5 | 402 | 0.87 | 0.95 | 65 | FAD, MLA |
Interfaces
16 interfaces between chains.
- G–H · 3139 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 3129 Ų buried · 51 hydrogen bonds · protein-protein
- J–K · 3129 Ų buried · 51 hydrogen bonds · protein-protein
- D–E · 3128 Ų buried · 51 hydrogen bonds · protein-protein
- I–L · 2159 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (flavinylation).
Compared structures
- 1E7P · QUINOL:FUMARATE reductase from wolinella succinogenes · 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 P17412
- Every structure of UniProt P17596
- Every structure of UniProt P17413
- Elsewhere: RCSB PDB 1E7P · PDBe 1E7P · UniProt P17412 · UniProt P17596 · UniProt P17413
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