Research workbench
Ethylbenzene dehydrogenase from aromatoleum aromaticum
Analyse Ethylbenzene dehydrogenase from aromatoleum aromaticum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IVF
- Type
- protein
- Length
- 1,463 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ethylbenzene dehydrogenase alpha-subunit; Ethylbenzene dehydrogenase beta-subunit…
- EC
- 1.17.99.2
- UniProt
- Q5P5I0, Q5P5I1, Q5P5I2
- Ligands
- SF4, MGD, MD1, F3S, HEM, MO, PO4
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ethylbenzene dehydrogenase alpha-subunit (EC 1.17.99.2) | protein | 912 | 36% helix, 17% strand | Q5P5I0 |
| B | Ethylbenzene dehydrogenase beta-subunit (EC 1.17.99.2) | protein | 337 | 26% helix, 19% strand | Q5P5I1 |
| C | Ethylbenzene dehydrogenase gamma-subunit (EC 1.17.99.2) | protein | 214 | 12% helix, 40% strand | Q5P5I2 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B
- MGD · 2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide · ligand · chains A
- MD1 · Phosphoric acid 4-(2-amino-4-oxo-3,4,5,6,-tetrahydro-pteridin-6-yl)-2-hydroxy-3,4-dimercapto-but-3-en-yl ester guanylate ester · ligand · chains A
- F3S · FE3-S4 cluster · ligand · chains B
- HEM · Protoporphyrin IX containing Fe · ligand · chains B, C
- MO · Molybdenum atom · metal · chains A
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 8 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.88 | 0.96 | 80 | ACT, SF4, MO, MGD |
| 2 | 252 | 0.82 | 0.94 | 38 | HEM |
| 3 | 165 | 0.81 | 0.97 | 39 | MO, MD1 |
| 4 | 287 | 0.73 | 0.86 | 44 | empty |
| 5 | 187 | 0.51 | 0.77 | 33 | empty |
Interfaces
2 interfaces between chains.
- A–B · 4369 Ų buried · 93 hydrogen bonds · protein-protein
- B–C · 1001 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2IVF · Ethylbenzene dehydrogenase from Aromatoleum aromaticum · 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 Q5P5I0
- Every structure of UniProt Q5P5I1
- Every structure of UniProt Q5P5I2
- Elsewhere: RCSB PDB 2IVF · PDBe 2IVF · UniProt Q5P5I0 · UniProt Q5P5I1 · UniProt Q5P5I2
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