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Crystal structure of MENAQUINOL:FUMARATE oxidoreductase in complex with a 3-nitropropionate adduct
Analyse Crystal structure of MENAQUINOL:FUMARATE oxidoreductase in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P4S
- 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 subunit; Fumarate…
- UniProt
- D3GV56, D3GV55, D3QL74, D3GV53
- Ligands
- FAD, FES, F3S, SF4, 3NP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M | Fumarate reductase flavoprotein subunit | protein | 577 | 38% helix, 20% strand | D3GV56 |
| B, N | Fumarate reductase iron-sulfur subunit | protein | 243 | 38% helix, 16% strand | D3GV55 |
| C, O | Fumarate reductase subunit C | protein | 130 | 71% helix, 4% strand | D3QL74 |
| D, P | Fumarate reductase subunit D | protein | 119 | 75% helix, 1% strand | D3GV53 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, 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
- 3NP · 3-nitropropanoic acid · ligand · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.86 | 0.95 | 56 | FAD, 3NP |
| 2 | 355 | 0.86 | 0.95 | 49 | FAD |
| 3 | 986 | 0.81 | 0.82 | 90 | empty |
| 4 | 792 | 0.80 | 0.83 | 61 | empty |
| 5 | 278 | 0.77 | 0.89 | 31 | empty |
Interfaces
13 interfaces between chains.
- M–N · 2754 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2692 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2347 Ų buried · 12 hydrogen bonds · protein-protein
- O–P · 2330 Ų buried · 11 hydrogen bonds · protein-protein
- N–O · 1450 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3P4S · Crystal structure of Menaquinol:fumarate oxidoreductase in complex with a… · 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
- Every structure of UniProt D3GV56
- Every structure of UniProt D3GV55
- Every structure of UniProt D3QL74
- Every structure of UniProt D3GV53
- Elsewhere: RCSB PDB 3P4S · PDBe 3P4S · UniProt D3GV56 · UniProt D3GV55 · UniProt D3QL74 · UniProt D3GV53
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