Research workbench
Structure of phosphoglycerate kinase (CBU_1782) from coxiella burnetii
Analyse Structure of phosphoglycerate kinase (CBU_1782) from coxiella burnetii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NG4
- Type
- protein
- Length
- 1,161 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase
- EC
- 2.7.2.3
- UniProt
- Q83AU6
- Ligands
- ADP, MG
- Pockets
- 12 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 384 | 43% helix, 18% strand | Q83AU6 |
| B | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 389 | 43% helix, 18% strand | Q83AU6 |
| C | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 388 | 44% helix, 18% strand | Q83AU6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.57 | 0.76 | 41 | empty |
| 2 | 197 | 0.57 | 0.80 | 35 | empty |
| 3 | 321 | 0.55 | 0.75 | 38 | empty |
| 4 | 149 | 0.54 | 0.81 | 21 | empty |
| 5 | 255 | 0.54 | 0.76 | 36 | empty |
Interfaces
3 interfaces between chains.
- B–C · 279 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 177 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 160 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4NG4 · Structure of phosphoglycerate kinase (CBU_1782) from Coxiella burnetii · the same entry in another collection · chain A against A, TM-score 1.00
- Q83AU6 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase (Q83AU6) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q83AU6
- Elsewhere: RCSB PDB 4NG4 · PDBe 4NG4 · UniProt Q83AU6
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