MolNFT v1 · #124483 · protein
2.45A resolution structure of apo independent phosphoglycerate mutase from C. elegans (orthorhombic form)
5KGL · 2,3-bisphosphoglycerate-independent phosphoglycerate mutase: “2.45A resolution structure of apo independent phosphoglycerate mutase from C. elegans (orthorhombic form)”. X-ray diffraction, 4 ligands (MN, ZN, SO4), 5 pockets (best…
- 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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