MolNFT v1 · #40114 · protein
Structure of a full-length homoprotocatechuate 2,3-dioxygenase from B. fuscum in a new spacegroup.
2IG9: “Structure of a full-length homoprotocatechuate 2,3-dioxygenase from B. fuscum in a new spacegroup.”. X-ray diffraction, 3 ligands (FE2, CA, CL), 20 pockets (best druggability 0.85). MolNFT v1 #40114 on GenesisL1: 3D structure…
- PDB
- 2IG9
- 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
- FE2, CA, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 16% 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 | 16% helix, 35% strand | Q45135 |
Ligands and binding sites
- FE2 · Fe (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 · 11 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 | 367 | 0.85 | 0.95 | 47 | empty |
| 2 | 356 | 0.84 | 0.94 | 43 | empty |
| 3 | 104 | 0.79 | 0.99 | 24 | GOL |
| 4 | 96 | 0.77 | 0.98 | 25 | GOL |
| 5 | 64 | 0.74 | 0.99 | 29 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1690 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 1686 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1682 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 1671 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 535 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2IG9 · Structure of a full-length Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in a new… · 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 2IG9 · PDBe 2IG9 · UniProt Q45135
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