Research workbench
Structure of mn-substituted homoprotocatechuate 2,3-dioxygenase from B.FUSCUM at 1.7 ang resolution
Analyse Structure of mn-substituted homoprotocatechuate 2,3-dioxygenase from B.FUSCUM… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BZA
- Type
- protein
- Length
- 1,436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homoprotocatechuate 2,3-dioxygenase
- EC
- 1.13.11.15
- UniProt
- Q45135
- Ligands
- MN, CA, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Homoprotocatechuate 2,3-dioxygenase (EC 1.13.11.15) | protein | 359 | 18% helix, 35% strand | Q45135 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, C, B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.85 | 0.94 | 46 | empty |
| 2 | 340 | 0.84 | 0.94 | 47 | empty |
| 3 | 100 | 0.78 | 0.98 | 23 | GOL |
| 4 | 97 | 0.77 | 0.98 | 25 | empty |
| 5 | 62 | 0.73 | 0.98 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1691 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 1689 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 1664 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1662 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 534 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3BZA · Structure of Mn-substituted Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.7 Ang… · 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 Q45135
- Elsewhere: RCSB PDB 3BZA · PDBe 3BZA · UniProt Q45135
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.