MolNFT v1 · #102161 · protein
2.6 ångström crystal structure of putative phosphoglycerate mutase 1 from toxoplasma gondii
4ODI · Phosphoglycerate mutase pgmii: “2.6 ångström crystal structure of putative phosphoglycerate mutase 1 from toxoplasma gondii”. X-ray diffraction, 1 ligand (NA), 12 pockets (best druggability 0.80). MolNFT v1 #102161 on GenesisL1: 3D…
- PDB
- 4ODI
- Type
- protein
- Length
- 966 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate mutase pgmii
- EC
- 5.4.2.4
- UniProt
- S8GJT7
- Ligands
- NA
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate mutase pgmii (EC 5.4.2.4) | protein | 246 | 45% helix, 14% strand | S8GJT7 |
| B | Phosphoglycerate mutase pgmii (EC 5.4.2.4) | protein | 245 | 45% helix, 14% strand | S8GJT7 |
| C | Phosphoglycerate mutase pgmii (EC 5.4.2.4) | protein | 243 | 45% helix, 14% strand | S8GJT7 |
| D | Phosphoglycerate mutase pgmii (EC 5.4.2.4) | protein | 232 | 44% helix, 15% strand | S8GJT7 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.80 | 0.81 | 104 | empty |
| 2 | 343 | 0.67 | 0.81 | 37 | empty |
| 3 | 604 | 0.65 | 0.76 | 50 | empty |
| 4 | 589 | 0.64 | 0.75 | 60 | NA |
| 5 | 417 | 0.64 | 0.78 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–C · 869 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 851 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 795 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 786 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 44 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ODI · 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 from Toxoplasma… · 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 S8GJT7
- Elsewhere: RCSB PDB 4ODI · PDBe 4ODI · UniProt S8GJT7
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