Research workbench
Glu C180 -> ile variant QUINOL:FUMARATE reductase from wolinella succinogenes
Analyse Glu C180 -> ile variant 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
- 2BS4
- Type
- protein
- Length
- 2,296 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Quinol-fumarate reductase flavoprotein subunit a; Quinol-fumarate reductase iron-sulfur…
- EC
- 1.3.99.1
- UniProt
- P17412, P17596, P17413
- Ligands
- HEM, FAD, F3S, FES, SF4, DMW, NA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Quinol-fumarate reductase flavoprotein subunit a (EC 1.3.99.1) | protein | 655 | 41% helix, 19% strand | P17412 |
| B, E | Quinol-fumarate reductase iron-sulfur subunit B (EC 1.3.99.1) | protein | 239 | 37% helix, 16% strand | P17596 |
| C, F | Quinol-fumarate reductase diheme cytochrome B subunit C (EC 1.3.99.1) | protein | 254 | 76% helix, 0% strand | P17413 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains B, C, E, F
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, D
- F3S · FE3-S4 cluster · ligand · 2 copies · chains B, E
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, E
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, E
- DMW · 2,3-dimethyl-1,4-naphthoquinone · ligand · 2 copies · chains C, F
- NA · Sodium ion · metal · 2 copies · chains D, A
- CIT · Citric acid · additive · 2 copies · chains A, D
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.89 | 0.92 | 75 | HEM, DMW |
| 2 | 721 | 0.89 | 0.92 | 66 | HEM, DMW |
| 3 | 394 | 0.86 | 0.94 | 64 | FAD, CIT |
| 4 | 400 | 0.85 | 0.94 | 64 | FAD, CIT |
| 5 | 987 | 0.81 | 0.82 | 90 | empty |
Interfaces
9 interfaces between chains.
- D–E · 2968 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2963 Ų buried · 50 hydrogen bonds · protein-protein
- C–F · 2083 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1646 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1644 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 2BS4 · Glu C180 -> ile variant QUINOL:FUMARATE reductase fromwolinella succinogenes · the same entry in another collection · chain E against E, TM-score 1.00
- P17413 · AlphaFold monomer V2.0 prediction for fumarate reductase cytochrome B subunit (P17413) · a predicted model of the same protein · chain F against A, TM-score 1.00
- P17596 · AlphaFold monomer V2.0 prediction for fumarate reductase iron-sulfur subunit (P17596) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P17412 · AlphaFold monomer V2.0 prediction for fumarate reductase flavoprotein subunit (P17412) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 2BS4 · PDBe 2BS4 · UniProt P17412 · UniProt P17596 · UniProt P17413
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