Research workbench
Crystal structure of QUINOL:FUMARATE reductase from desulfovibrio gigas
Analyse Crystal structure of QUINOL:FUMARATE reductase from desulfovibrio gigas in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XMJ
- Type
- protein
- Length
- 4,296 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate reductase flavoprotein subunit; Succinate dehydrogenase iron-sulfur subunit…
- EC
- 1.3.5.1
- Ligands
- HEM, FAD, FUM, F3S, SF4, FES, MQ7
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Fumarate reductase flavoprotein subunit | protein | 622 | 33% helix, 20% strand | — |
| B, F, J, N | Succinate dehydrogenase iron-sulfur subunit (EC 1.3.5.1) | protein | 240 | 34% helix, 16% strand | — |
| C, G, K, O | Fumarate reductase respiratory complex | protein | 212 | 69% helix, 0% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains C, B, G, F, K, J, O, N
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, E, I, M
- FUM · Fumaric acid · ligand · 4 copies · chains A, E, I, M
- F3S · FE3-S4 cluster · ligand · 4 copies · chains B, F, J, N
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains B, F, J, N
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains B, F, J, N
- MQ7 · Menaquinone-7 · ligand · chains C
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains C, O
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 | 938 | 0.88 | 0.90 | 90 | HEM |
| 2 | 544 | 0.88 | 0.94 | 81 | HEM |
| 3 | 567 | 0.88 | 0.93 | 72 | HEM |
| 4 | 1007 | 0.87 | 0.87 | 98 | HEM |
| 5 | 383 | 0.86 | 0.95 | 64 | FAD, FUM |
Interfaces
17 interfaces between chains.
- A–B · 2961 Ų buried · 31 hydrogen bonds · protein-protein
- M–N · 2931 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2886 Ų buried · 38 hydrogen bonds · protein-protein
- I–J · 2859 Ų buried · 40 hydrogen bonds · protein-protein
- F–G · 1728 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent, 4 cofactor (covalent ligand, flavinylation).
Compared structures
- 5XMJ · Crystal structure of quinol:fumarate reductase from Desulfovibrio gigas · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 5XMJ · PDBe 5XMJ
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