Research workbench
Crystal structure of phosphoglycerate kinase from streptococcus pneumoniae
Analyse Crystal structure of phosphoglycerate kinase from streptococcus pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZLB
- Type
- protein
- Length
- 398 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase
- EC
- 2.7.2.3
- UniProt
- Q04LZ5
- Ligands
- ANP, MG
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 398 | 40% helix, 16% strand | Q04LZ5 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.45 | 0.77 | 33 | ANP, MG |
| 2 | 74 | 0.39 | 0.78 | 23 | GOL |
Compared structures
- 3ZLB · Crystal structure of phosphoglycerate kinase from Streptococcus pneumoniae · the same entry in another collection · chain A against A, TM-score 1.00
- Q04LZ5 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase (Q04LZ5) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q04LZ5
- Elsewhere: RCSB PDB 3ZLB · PDBe 3ZLB · UniProt Q04LZ5
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