MolNFT v1 · #61996 · protein
The 1.4 a crystal structure of the large and cold-active vibrio sp. alkaline phosphatase
3E2D: “The 1.4 a crystal structure of the large and cold-active vibrio sp. alkaline phosphatase”. X-ray diffraction, 3 ligands (ZN, MG, SO4), 8 pockets (best druggability 0.67). MolNFT v1 #61996 on GenesisL1: 3D structure, binding sites…
- PDB
- 3E2D
- Type
- protein
- Length
- 1,004 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline phosphatase
- EC
- 3.1.3.1
- UniProt
- Q93P54
- Ligands
- ZN, MG, SO4
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alkaline phosphatase (EC 3.1.3.1) | protein | 502 | 40% helix, 17% strand | Q93P54 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.67 | 0.78 | 59 | ZN, SO4 |
| 2 | 490 | 0.67 | 0.78 | 48 | SO4, EDO |
| 3 | 87 | 0.39 | 0.77 | 23 | empty |
| 4 | 78 | 0.37 | 0.77 | 19 | EDO |
| 5 | 85 | 0.37 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4462 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 3E2D · The 1.4 A crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase · 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 Q93P54
- Elsewhere: RCSB PDB 3E2D · PDBe 3E2D · UniProt Q93P54
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