Research workbench
Crystal structure of tpado in a substrate-free state
Analyse Crystal structure of tpado in a substrate-free state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q04
- Type
- protein
- Length
- 1,741 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1; Terephthalate…
- EC
- 1.14.12.15, 3.2.1.17
- UniProt
- Q3C1E2, Q3C1D5, P00698
- Ligands
- FES, FE
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1 (EC 1.14.12.15) | protein | 154 | 27% helix, 45% strand | Q3C1E2 |
| D | Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2 (EC 1.14.12.15) | protein | 374 | 25% helix, 30% strand | Q3C1D5 |
| E | Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2 (EC 1.14.12.15) | protein | 400 | 26% helix, 29% strand | Q3C1D5 |
| F | Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2 (EC 1.14.12.15) | protein | 376 | 24% helix, 30% strand | Q3C1D5 |
| H | Lysozyme (EC 3.2.1.17) | protein | 129 | 43% helix, 11% strand | P00698 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains D, E, F
- FE · Fe (III) ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.81 | 0.86 | 77 | empty |
| 2 | 1137 | 0.80 | 0.81 | 126 | empty |
| 3 | 518 | 0.79 | 0.86 | 77 | empty |
| 4 | 486 | 0.79 | 0.87 | 67 | empty |
| 5 | 681 | 0.79 | 0.84 | 80 | empty |
Interfaces
14 interfaces between chains.
- B–E · 1611 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1579 Ų buried · 30 hydrogen bonds · protein-protein
- C–F · 1538 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 1348 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1298 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7Q04 · Crystal structure of TPADO in a substrate-free state · the same entry in another collection · chain H against H, TM-score 1.00
- Q3C1D5 · AlphaFold monomer V2.0 prediction for terephthalate 1,2-dioxygenase, terminal oxygenase… · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q3C1E2 · AlphaFold monomer V2.0 prediction for terephthalate 1,2-dioxygenase, terminal oxygenase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q3C1E2
- Every structure of UniProt Q3C1D5
- Every structure of UniProt P00698
- Elsewhere: RCSB PDB 7Q04 · PDBe 7Q04 · UniProt Q3C1E2 · UniProt Q3C1D5 · UniProt P00698
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