Research workbench
Crystal structure of aphc in complex with 4-ethylcatechol
Analyse Crystal structure of aphc in complex with 4-ethylcatechol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q2A
- Type
- protein
- Length
- 1,399 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol 2,3-dioxygenase
- EC
- 1.13.11.2
- UniProt
- Q0S9X1
- Ligands
- 8RU, CA, FE
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 350 | 23% helix, 33% strand | Q0S9X1 |
| B | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 352 | 23% helix, 34% strand | Q0S9X1 |
| C | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 347 | 23% helix, 34% strand | Q0S9X1 |
| D | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 350 | 23% helix, 33% strand | Q0S9X1 |
Ligands and binding sites
- 8RU · 4-ethylbenzene-1,2-diol · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.83 | 0.97 | 58 | empty |
| 2 | 121 | 0.80 | 0.98 | 30 | FE, 8RU |
| 3 | 100 | 0.79 | 0.99 | 28 | FE, 8RU |
| 4 | 105 | 0.79 | 0.98 | 29 | 8RU |
| 5 | 95 | 0.78 | 0.98 | 29 | 8RU |
Interfaces
6 interfaces between chains.
- A–C · 1994 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1982 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1067 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1056 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 847 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7Q2A · Crystal structure of AphC in complex with 4-ethylcatechol · 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 Q0S9X1
- Elsewhere: RCSB PDB 7Q2A · PDBe 7Q2A · UniProt Q0S9X1
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