Research workbench
2.95A resolution structure of apo independent phosphoglycerate mutase from C. elegans (monoclinic form)
Analyse 2.95A 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
- 5KGM
- Type
- protein
- Length
- 1,037 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, CL
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) | protein | 519 | 38% helix, 17% strand | G5EFZ1 |
| B | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) | protein | 518 | 37% helix, 18% 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
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.81 | 0.89 | 52 | MN |
| 2 | 703 | 0.70 | 0.77 | 67 | empty |
| 3 | 356 | 0.57 | 0.76 | 36 | empty |
| 4 | 204 | 0.56 | 0.79 | 20 | empty |
| 5 | 89 | 0.46 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1107 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5KGM · 2.95A 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 B against A, TM-score 0.87
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 5KGM · PDBe 5KGM · UniProt G5EFZ1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.