MolNFT v1 · #4500 · protein
Three-dimensional structure of a novel phospholipase A2 from indian common krait at 2.45 a resolution
1DPY: “Three-dimensional structure of a novel phospholipase A2 from indian common krait at 2.45 a resolution”. X-ray diffraction, 1 ligand (NA), 1 pocket (best druggability 0.53). MolNFT v1 #4500 on GenesisL1: 3D structure, binding sites…
- PDB
- 1DPY
- Type
- protein
- Length
- 117 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- Q9DF52
- Ligands
- NA
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 (EC 3.1.1.4) | protein | 117 | 45% helix, 9% strand | Q9DF52 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.53 | 0.78 | 18 | NA |
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1DPY · Three-dimensional structure of a novel phospholipase A2 from indian common krait at 2.45… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9DF52 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 KPA2 (Q9DF52) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9DF52
- Elsewhere: RCSB PDB 1DPY · PDBe 1DPY · UniProt Q9DF52
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