Research workbench
A new form of catalytically inactive phospholipase A2 with an unusual disulphide bridge cys 32- cys 49 reveals recognition for N- acetylglucosmine
Analyse A new form of catalytically inactive phospholipase A2 with an unusual… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y75
- Type
- protein
- Length
- 236 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 isoform 5; Phospholipase A2 isoform 6
- EC
- 3.1.1.4
- UniProt
- Q5G291, Q5G290
- Ligands
- NAG, ZN
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 isoform 5 (EC 3.1.1.4) | protein | 118 | 48% helix, 9% strand | Q5G291 |
| B | Phospholipase A2 isoform 6 (EC 3.1.1.4) | protein | 118 | 48% helix, 9% strand | Q5G290 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
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 | 1068 | 0.81 | 0.82 | 71 | NAG |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 1Y75 · A new form of catalytically inactive phospholipase A2 with an unusual disulphide bridge… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5G290 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 6 (Q5G290) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q5G291 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 5 (Q5G291) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q5G291
- Every structure of UniProt Q5G290
- Elsewhere: RCSB PDB 1Y75 · PDBe 1Y75 · UniProt Q5G291 · UniProt Q5G290
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