MolNFT v1 · #1541 · protein
Basic phospholipase A2 from agkistrodon halys pallas-implications for its association and anticoagulant activities by X-ray crystallography
1B4W · Protein (phospholipase A2): “Basic phospholipase A2 from agkistrodon halys pallas-implications for its association and anticoagulant…”. X-ray diffraction, 7 pockets (best druggability 0.81). MolNFT v1 #1541 on GenesisL1: 3D…
- PDB
- 1B4W
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (phospholipase A2)
- EC
- 3.1.1.4
- UniProt
- O42187
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein (phospholipase A2) (EC 3.1.1.4) | protein | 122 | 51% helix, 3% strand | O42187 |
Ligands and binding sites
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.81 | 0.93 | 37 | BOG |
| 2 | 183 | 0.77 | 0.93 | 35 | BOG |
| 3 | 181 | 0.77 | 0.92 | 37 | empty |
| 4 | 167 | 0.77 | 0.93 | 28 | empty |
| 5 | 86 | 0.66 | 0.92 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–D · 814 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 803 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 433 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 312 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 237 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 1B4W · Basic phospholipase A2 from agkistrodon halys pallas-implications for its association and… · the same entry in another collection · chain A against A, TM-score 1.00
- O42187 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 B (O42187) · 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 O42187
- Elsewhere: RCSB PDB 1B4W · PDBe 1B4W · UniProt O42187
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