MolNFT v1 · #124485 · protein
1.95A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (2D)
5KGN · 2,3-bisphosphoglycerate-independent phosphoglycerate mutase: “1.95A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a…”. X-ray diffraction, 6 ligands (ACE, MG, MN), 7 pockets (best…
- PDB
- 5KGN
- Type
- protein
- Length
- 1,073 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Macrocyclic peptide inhibitor
- EC
- 5.4.2.12
- UniProt
- G5EFZ1
- Ligands
- ACE, MG, MN, ZN, NH2, CL
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) | protein | 530 | 40% helix, 17% strand | G5EFZ1 |
| B | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) | protein | 521 | 39% helix, 18% strand | G5EFZ1 |
| C, D | Macrocyclic peptide inhibitor | protein | 11 | 36% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.77 | 0.81 | 85 | empty |
| 2 | 294 | 0.66 | 0.82 | 45 | empty |
| 3 | 170 | 0.64 | 0.85 | 35 | empty |
| 4 | 81 | 0.41 | 0.78 | 15 | empty |
| 5 | 85 | 0.41 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1036 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 754 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 750 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 d-amino (covalent ligand, D-amino acid).
Compared structures
- 5KGN · 1.95A resolution structure of independent phosphoglycerate mutase from C. elegans in… · 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 0.96
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 5KGN · PDBe 5KGN · UniProt G5EFZ1
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