Research workbench
Pseudomonas fluorescens phox in complex with the substrate analogue appcp
Analyse Pseudomonas fluorescens phox in complex with the substrate analogue appcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AMF
- Type
- protein
- Length
- 1,162 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phox
- EC
- 3.1.3.1
- UniProt
- Q3K5N8
- Ligands
- ACP, FEO, CA, LI, CL
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phox (EC 3.1.3.1) | protein | 581 | 13% helix, 34% strand | Q3K5N8 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- FEO · Mu-oxo-diiron · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- LI · Lithium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.81 | 0.82 | 91 | EDO |
| 2 | 455 | 0.70 | 0.81 | 35 | EDO |
| 3 | 448 | 0.70 | 0.81 | 33 | EDO |
| 4 | 341 | 0.70 | 0.83 | 39 | empty |
| 5 | 370 | 0.57 | 0.76 | 47 | ACP, CA, FEO |
Interfaces
1 interface between chains.
- A–B · 723 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4AMF · Pseudomonas fluorescens PhoX in complex with the substrate analogue AppCp · 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 Q3K5N8
- Elsewhere: RCSB PDB 4AMF · PDBe 4AMF · UniProt Q3K5N8
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