MolNFT v1 · #180041 · protein
1.80A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (ce-1 nhoh)
7KNF · 2,3-bisphosphoglycerate-independent phosphoglycerate mutase: “1.80A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a…”. X-ray diffraction, 4 ligands (ACE, HOA, ZN), 6 pockets (best…
- PDB
- 7KNF
- Type
- protein
- Length
- 1,037 residues
- Chains
- 4
- 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
- ACE, HOA, ZN, NA
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) | protein | 506 | 39% helix, 18% strand | G5EFZ1 |
| B | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) | protein | 505 | 38% helix, 18% strand | G5EFZ1 |
| C, D | Dty-asp-tyr-pro-gly-asp-his-cys-tyr-leu-tyr-gly-thr | protein | 13 | 31% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains C, D
- HOA · Hydroxyamine · ligand · 2 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 4 copies · chains A, C, B, D
- NA · Sodium ion · metal · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.72 | 0.76 | 91 | empty |
| 2 | 273 | 0.59 | 0.79 | 43 | PG4 |
| 3 | 122 | 0.53 | 0.82 | 24 | PG4 |
| 4 | 119 | 0.44 | 0.78 | 20 | empty |
| 5 | 82 | 0.42 | 0.79 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–D · 816 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 815 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 810 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 4 modified, 2 d-amino (covalent ligand, oxidation, D-amino acid).
Compared structures
- 7KNF · 1.80A 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 7KNF · PDBe 7KNF · UniProt G5EFZ1
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