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Crystal structure of 2,3-dihydroxy biphenyl dioxygenase from rhodococcus sp. (strain RHA1)
Analyse Crystal structure of 2,3-dihydroxy biphenyl dioxygenase from rhodococcus sp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LM4
- Type
- protein
- Length
- 1,304 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
- PEO, HPX, FE
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 325 | 22% helix, 36% strand | Q0S9X1 |
| B | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 326 | 21% helix, 36% strand | Q0S9X1 |
| D | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 328 | 22% helix, 36% strand | Q0S9X1 |
Ligands and binding sites
- PEO · Hydrogen peroxide · ligand · 4 copies · chains A, B, C, D
- HPX · (2Z,4E)-2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid · ligand · 4 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
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.84 | 0.97 | 61 | empty |
| 2 | 214 | 0.83 | 0.96 | 54 | empty |
| 3 | 447 | 0.77 | 0.86 | 52 | empty |
| 4 | 399 | 0.75 | 0.85 | 58 | empty |
| 5 | 135 | 0.75 | 0.93 | 29 | FE, PEO, HPX |
Interfaces
6 interfaces between chains.
- A–C · 1978 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1976 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1043 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1038 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 736 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3LM4 · Crystal Structure of 2,3-Dihydroxy Biphenyl dioxygenase from Rhodococcus sp. (strain RHA1) · 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 3LM4 · PDBe 3LM4 · UniProt Q0S9X1
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