MolNFT v1 · #31994 · protein
A possible role of the second calcium ion in interfacial binding: atomic and medium resolution crystal structures of the quadruple mutant of phospholipase A2
2BD1: “A possible role of the second calcium ion in interfacial binding: atomic and medium resolution crystal…”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.76). MolNFT v1 #31994 on GenesisL1: 3D structure, binding…
- PDB
- 2BD1
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P00593
- Ligands
- CA
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 (EC 3.1.1.4) | protein | 123 | 46% helix, 7% strand | P00593 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.76 | 0.79 | 71 | MPD |
| 2 | 181 | 0.62 | 0.83 | 23 | MPD |
Interfaces
1 interface between chains.
- A–B · 346 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2BD1 · A possible role of the second calcium ion in interfacial binding: Atomic and medium… · the same entry in another collection · chain A against A, TM-score 1.00
- P00593 · AlphaFold monomer V2.0 prediction for phospholipase A2 (P00593) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00593
- Elsewhere: RCSB PDB 2BD1 · PDBe 2BD1 · UniProt P00593
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