MolNFT v1 · #50262 · protein
Design of specific inhibitors of phospholipase A2: crystal structure of the complex of phospholipase A2 with pentapeptide leu-val-phe-phe- ala at 2.9 a resolution
2RD4 · Phospholipase A2 isoform 1: “Design of specific inhibitors of phospholipase A2: crystal structure of the complex of phospholipase A2 with…”. X-ray diffraction, 1 ligand (CA), 1 pocket (best druggability 0.75). MolNFT v1 #50262 on…
- PDB
- 2RD4
- Type
- protein
- Length
- 243 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 isoform 1; Phospholipase A2 isoform 2; Pentapeptide inhibitor
- EC
- 3.1.1.4
- UniProt
- P60043, P60044
- Ligands
- CA
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 isoform 1 (EC 3.1.1.4) | protein | 119 | 48% helix, 8% strand | P60043 |
| B | Phospholipase A2 isoform 2 (EC 3.1.1.4) | protein | 119 | 49% helix, 9% strand | P60044 |
| C | Pentapeptide inhibitor | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B, C
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 | 547 | 0.75 | 0.82 | 57 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1037 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 524 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 165 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 2RD4 · Design of specific inhibitors of Phospholipase A2: Crystal structure of the complex of… · the same entry in another collection · chain A against A, TM-score 1.00
- P60043 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 1 (P60043) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P60044 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 2 (P60044) · a predicted model of the same protein · chain B 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 P60043
- Every structure of UniProt P60044
- Elsewhere: RCSB PDB 2RD4 · PDBe 2RD4 · UniProt P60043 · UniProt P60044
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