MolNFT v1 · #1341 · protein
A probe molecule composed of seventeen percent of total diffracting matter gives correct solutions in molecular replacement
1AYP · Phospholipase A2: “A probe molecule composed of seventeen percent of total diffracting matter gives correct solutions in…”. X-ray diffraction, 2 ligands (INB, CA), 8 pockets (best druggability 0.81). MolNFT v1 #1341 on GenesisL1: 3D…
- PDB
- 1AYP
- Type
- protein
- Length
- 744 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P14555
- Ligands
- INB, CA
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Phospholipase A2 (EC 3.1.1.4) | protein | 124 | 47% helix, 7% strand | P14555 |
Ligands and binding sites
- INB · 1-octadecyl-2-acetamido-2-deoxy-sn-glycerol-3-phosphoethylmethyl sulfide · ligand · 6 copies · chains A, D, B, F, C, E
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.81 | 0.83 | 102 | INB |
| 2 | 410 | 0.75 | 0.85 | 58 | INB |
| 3 | 332 | 0.74 | 0.86 | 38 | INB |
| 4 | 563 | 0.74 | 0.82 | 64 | INB |
| 5 | 329 | 0.70 | 0.83 | 44 | INB |
Interfaces
12 interfaces between chains.
- B–F · 477 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 388 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 386 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 348 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 327 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 1AYP · A probe molecule composed of seventeen percent of total diffracting matter gives correct… · the same entry in another collection · chain C against C, TM-score 1.00
- P14555 · AlphaFold monomer V2.0 prediction for phospholipase A2, membrane associated (P14555) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P14555
- Elsewhere: RCSB PDB 1AYP · PDBe 1AYP · UniProt P14555
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