MolNFT v1 · #72705 · protein
Crystal structure of a putative deoxyribose-phosphate aldolase from entamoeba histolytica
3NGJ: “Crystal structure of a putative deoxyribose-phosphate aldolase from entamoeba histolytica”. X-ray diffraction, 2 ligands (ZN, NA), 10 pockets (best druggability 0.78). MolNFT v1 #72705 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3NGJ
- Type
- protein
- Length
- 879 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose-phosphate aldolase
- UniProt
- C4M5C6
- Ligands
- ZN, NA
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxyribose-phosphate aldolase | protein | 218 | 50% helix, 18% strand | C4M5C6 |
| C | Deoxyribose-phosphate aldolase | protein | 221 | 48% helix, 18% strand | C4M5C6 |
| D | Deoxyribose-phosphate aldolase | protein | 222 | 49% helix, 18% strand | C4M5C6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.78 | 0.84 | 78 | EDO |
| 2 | 483 | 0.76 | 0.84 | 58 | empty |
| 3 | 79 | 0.76 | 0.99 | 24 | empty |
| 4 | 86 | 0.76 | 0.98 | 25 | empty |
| 5 | 111 | 0.59 | 0.85 | 27 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1372 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1342 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 264 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 256 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 163 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3NGJ · Crystal structure of a putative deoxyribose-phosphate aldolase from Entamoeba histolytica · 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 C4M5C6
- Elsewhere: RCSB PDB 3NGJ · PDBe 3NGJ · UniProt C4M5C6
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