MolNFT v1 · #188291 · protein
1.90A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a macrocyclic peptide inhibitor (sa-D2)
7TL7 · 2,3-bisphosphoglycerate-independent phosphoglycerate mutase: “1.90A resolution structure of independent phosphoglycerate mutase from C. elegans in complex with a…”. X-ray diffraction, 4 ligands (ACE, ZN, NA), 15 pockets (best…
- PDB
- 7TL7
- Type
- protein
- Length
- 2,152 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Peptide sa-D2
- EC
- 5.4.2.12
- UniProt
- G5EFZ1
- Ligands
- ACE, ZN, NA, NH2
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 5 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 | 531 | 39% helix, 18% strand | G5EFZ1 |
| B | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) | protein | 526 | 37% helix, 18% strand | G5EFZ1 |
| C | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) | protein | 522 | 38% helix, 19% strand | G5EFZ1 |
| D | 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.12) | protein | 521 | 38% helix, 18% strand | G5EFZ1 |
| a, b, c, d | Peptide sa-D2 | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, a, B, b, C, c, D, d
- ZN · Zinc ion · metal · 8 copies · chains A, a, B, b, C, c, D, d
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- NH2 · Amino group · ion · 4 copies · chains A, a, B, b, C, c, D, d
- IMD · Imidazole · additive · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.83 | 0.84 | 112 | empty |
| 2 | 743 | 0.79 | 0.83 | 85 | empty |
| 3 | 212 | 0.65 | 0.84 | 36 | empty |
| 4 | 251 | 0.54 | 0.77 | 35 | empty |
| 5 | 114 | 0.53 | 0.82 | 26 | empty |
Interfaces
8 interfaces between chains.
- A–C · 826 Ų buried · 5 hydrogen bonds · protein-protein
- A–a · 691 Ų buried · 8 hydrogen bonds · protein-protein
- B–b · 691 Ų buried · 9 hydrogen bonds · protein-protein
- D–d · 672 Ų buried · 8 hydrogen bonds · protein-protein
- C–c · 668 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 8 modified, 4 d-amino (covalent ligand, nonstandard, D-amino acid).
Compared structures
- 7TL7 · 1.90A resolution structure of independent phosphoglycerate mutase from C. elegans in… · the same entry in another collection · chain d against d, TM-score 1.00
- G5EFZ1 · AlphaFold monomer V2.0 prediction for 2,3-bisphosphoglycerate- independent… · a predicted model of the same protein · chain C against A, TM-score 0.97
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 7TL7 · PDBe 7TL7 · UniProt G5EFZ1
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