MolNFT v1 · #48053 · protein
Crystal structure determination of a salicylate 1,2-dioxygenase from pseudaminobacter salicylatoxidans
2PHD · Gentisate 1,2-dioxygenase: “Crystal structure determination of a salicylate 1,2-dioxygenase from pseudaminobacter salicylatoxidans”. X-ray diffraction, 2 ligands (FE, CL), 20 pockets (best druggability 0.73). MolNFT v1 #48053 on…
- PDB
- 2PHD
- Type
- protein
- Length
- 1,397 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gentisate 1,2-dioxygenase
- EC
- 1.13.11.4
- UniProt
- Q67FT0
- Ligands
- FE, CL
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gentisate 1,2-dioxygenase (EC 1.13.11.4) | protein | 349 | 17% helix, 36% strand | Q67FT0 |
| B | Gentisate 1,2-dioxygenase (EC 1.13.11.4) | protein | 348 | 18% helix, 36% strand | Q67FT0 |
| C | Gentisate 1,2-dioxygenase (EC 1.13.11.4) | protein | 348 | 18% helix, 37% strand | Q67FT0 |
| D | Gentisate 1,2-dioxygenase (EC 1.13.11.4) | protein | 352 | 20% helix, 38% strand | Q67FT0 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 2 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.73 | 0.98 | 23 | empty |
| 2 | 64 | 0.72 | 0.98 | 18 | empty |
| 3 | 209 | 0.70 | 0.87 | 35 | FE, ACT |
| 4 | 258 | 0.69 | 0.85 | 33 | ACT |
| 5 | 215 | 0.68 | 0.85 | 32 | FE |
Interfaces
4 interfaces between chains.
- A–C · 3669 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 3590 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1776 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1715 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2PHD · Crystal Structure Determination of a Salicylate 1,2-Dioxygenase from Pseudaminobacter… · 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 Q67FT0
- Elsewhere: RCSB PDB 2PHD · PDBe 2PHD · UniProt Q67FT0
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