Research workbench
2.45A resolution structure of apo independent phosphoglycerate mutase from C. elegans (orthorhombic form)
Analyse 2.45A resolution structure of apo independent phosphoglycerate mutase from C.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KGL
- Type
- protein
- Length
- 1,040 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
- EC
- 5.4.2.12
- UniProt
- G5EFZ1
- Ligands
- MN, ZN, SO4, CL
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) | protein | 520 | 37% helix, 16% strand | G5EFZ1 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.69 | 0.81 | 43 | empty |
| 2 | 1090 | 0.69 | 0.74 | 81 | empty |
| 3 | 101 | 0.47 | 0.80 | 16 | empty |
| 4 | 81 | 0.41 | 0.78 | 13 | empty |
| 5 | 93 | 0.32 | 0.72 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 601 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5KGL · 2.45A resolution structure of Apo independent phosphoglycerate mutase from C. elegans… · the same entry in another collection · chain A against A, TM-score 1.00
- G5EFZ1 · AlphaFold monomer V2.0 prediction for 2,3-bisphosphoglycerate- independent… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 G5EFZ1
- Elsewhere: RCSB PDB 5KGL · PDBe 5KGL · UniProt G5EFZ1
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