Research workbench
1.37 ångström resolution crystal structure of apo-form of a putative deoxyribose-phosphate aldolase from toxoplasma gondii ME49
Analyse 1.37 ångström resolution crystal structure of apo-form of a putative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EIV
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose-phosphate aldolase
- EC
- 4.1.2.4
- UniProt
- B9PVB4
- Ligands
- CL
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 256 | 54% helix, 15% strand | B9PVB4 |
| B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 256 | 55% helix, 14% strand | B9PVB4 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.69 | 0.88 | 24 | CL |
| 2 | 52 | 0.52 | 0.88 | 17 | empty |
| 3 | 99 | 0.44 | 0.79 | 28 | empty |
| 4 | 67 | 0.43 | 0.82 | 21 | empty |
| 5 | 80 | 0.41 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1242 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 4EIV · 1.37 Angstrom resolution crystal structure of apo-form of a putative… · 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 B9PVB4
- Elsewhere: RCSB PDB 4EIV · PDBe 4EIV · UniProt B9PVB4
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