Research workbench
Crystal structure of yersinia pestis hppk (ternary complex)
Analyse Crystal structure of yersinia pestis hppk (ternary complex) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QX0
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7,8-dihydro-6-hydroxymethylpterin- pyrophosphokinase
- EC
- 2.7.6.3
- UniProt
- Q7CKD7
- Ligands
- APC, PH2, MG
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 7,8-dihydro-6-hydroxymethylpterin- pyrophosphokinase (EC 2.7.6.3) | protein | 159 | 31% helix, 28% strand | Q7CKD7 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- PH2 · 2-amino-6-hydroxymethyl-7,8-dihydro-3H-pteridin-4-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.84 | 0.85 | 77 | MG, APC, PH2 |
| 2 | 252 | 0.55 | 0.76 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1411 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2QX0 · Crystal Structure of Yersinia pestis HPPK (Ternary Complex) · 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 Q7CKD7
- Elsewhere: RCSB PDB 2QX0 · PDBe 2QX0 · UniProt Q7CKD7
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