MolNFT v1 · #137477 · protein
Crystal structure of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase bound to 3-phosphoglycerate, from acinetobacter baumannii
5VPU: “Crystal structure of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase bound to 3-phosphoglycerate…”. X-ray diffraction, 2 ligands (3PG, MN), 5 pockets (best druggability 0.72). MolNFT v1 #137477 on GenesisL1: 3D…
- PDB
- 5VPU
- Type
- protein
- Length
- 509 residues
- Chains
- 1
- 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
- A0A059ZPG7
- Ligands
- 3PG, MN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 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 | 509 | 38% helix, 18% strand | A0A059ZPG7 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
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 | 181 | 0.72 | 0.90 | 30 | empty |
| 2 | 89 | 0.65 | 0.91 | 28 | EDO |
| 3 | 96 | 0.45 | 0.80 | 19 | empty |
| 4 | 51 | 0.41 | 0.82 | 17 | empty |
| 5 | 111 | 0.34 | 0.72 | 17 | empty |
Compared structures
- 5VPU · Crystal Structure of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase bound to… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A059ZPG7
- Elsewhere: RCSB PDB 5VPU · PDBe 5VPU · UniProt A0A059ZPG7
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