Research workbench
Crystal structure of mitochondrial respiratory complex II bound with 3-nitropropionate and 2-thenoyltrifluoroacetone
Analyse Crystal structure of mitochondrial respiratory complex II bound with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZP0
- Type
- protein
- Length
- 1,092 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FAD-binding protein; Iron-sulfur protein; Large cytochrome binding protein; Small…
- EC
- 1.3.5.1
- Ligands
- TTF, FAD, 3NP, FES, SF4, F3S, HEM
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FAD-binding protein (EC 1.3.5.1) | protein | 613 | 32% helix, 22% strand | — |
| B | Iron-sulfur protein (EC 1.3.5.1) | protein | 239 | 28% helix, 15% strand | — |
| C | Large cytochrome binding protein | protein | 138 | 74% helix, 1% strand | — |
| D | Small cytochrome binding protein | protein | 102 | 85% helix, 0% strand | — |
Ligands and binding sites
- TTF · 4,4,4-trifluoro-1-thien-2-ylbutane-1,3-dione · ligand · 2 copies · chains B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · chains A, B
- 3NP · 3-nitropropanoic acid · ligand · chains A
- FES · Fe2/s2 (inorganic) cluster · ligand · chains B
- SF4 · Iron/sulfur cluster · ligand · chains B
- F3S · FE3-S4 cluster · ligand · chains B
- HEM · Protoporphyrin IX containing Fe · ligand · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.86 | 0.95 | 62 | FAD, 3NP |
| 2 | 1114 | 0.85 | 0.85 | 102 | HEM, TTF |
| 3 | 91 | 0.74 | 0.96 | 21 | empty |
| 4 | 56 | 0.72 | 0.98 | 17 | SF4 |
| 5 | 377 | 0.72 | 0.83 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2724 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 1717 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1311 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 627 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 104 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 disulfide (flavinylation, disulfide).
Compared structures
- 1ZP0 · Crystal Structure of Mitochondrial Respiratory Complex II bound with 3-nitropropionate… · 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 1ZP0 · PDBe 1ZP0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.