Research workbench
Intradiol ring-cleavage dioxygenase from tetranychus urticae
Analyse Intradiol ring-cleavage dioxygenase from tetranychus urticae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VG2
- Type
- protein
- Length
- 812 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intradiol ring-cleavage dioxygenase
- UniProt
- T1K8P1
- Ligands
- FE
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | Intradiol ring-cleavage dioxygenase | protein | 203 | 13% helix, 29% strand | T1K8P1 |
| A, C | Intradiol ring-cleavage dioxygenase | protein | 204 | 13% helix, 29% strand | T1K8P1 |
| B | Intradiol ring-cleavage dioxygenase | protein | 201 | 13% helix, 30% strand | T1K8P1 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains U, A, B, C
- CAC · Cacodylate ion · additive · 9 copies · chains U, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.80 | 0.81 | 132 | empty |
| 2 | 65 | 0.37 | 0.78 | 15 | empty |
| 3 | 50 | 0.35 | 0.79 | 15 | empty |
| 4 | 87 | 0.34 | 0.75 | 14 | empty |
| 5 | 64 | 0.31 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 370 Ų buried · 7 hydrogen bonds · protein-protein
- U–C · 370 Ų buried · 7 hydrogen bonds · protein-protein
- U–B · 359 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 352 Ų buried · 2 hydrogen bonds · protein-protein
- U–A · 314 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5VG2 · Intradiol ring-cleavage Dioxygenase from Tetranychus urticae · the same entry in another collection · chain U against U, 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 T1K8P1
- Elsewhere: RCSB PDB 5VG2 · PDBe 5VG2 · UniProt T1K8P1
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