MolNFT v1 · #93383 · protein
Crystal structure analysis of a basic phospholipase A2 from trimeresurus stejnegeri venom
4H0S · Basic phospholipase A2 homolog cts-R6: “Crystal structure analysis of a basic phospholipase A2 from trimeresurus stejnegeri venom”. X-ray diffraction, 1 ligand (NA), 4 pockets (best druggability 0.54). MolNFT v1 #93383 on GenesisL1…
- PDB
- 4H0S
- Type
- protein
- Length
- 345 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic phospholipase A2 homolog cts-R6
- EC
- 3.1.1.4
- UniProt
- Q6H3D7
- Ligands
- NA
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Basic phospholipase A2 homolog cts-R6 (EC 3.1.1.4) | protein | 118 | 47% helix, 8% strand | Q6H3D7 |
| B | Basic phospholipase A2 homolog cts-R6 (EC 3.1.1.4) | protein | 114 | 47% helix, 7% strand | Q6H3D7 |
| C | Basic phospholipase A2 homolog cts-R6 (EC 3.1.1.4) | protein | 113 | 46% helix, 9% strand | Q6H3D7 |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.54 | 0.78 | 25 | NA |
| 2 | 169 | 0.54 | 0.79 | 24 | empty |
| 3 | 144 | 0.54 | 0.80 | 20 | empty |
| 4 | 88 | 0.38 | 0.76 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 592 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 434 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 136 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 4H0S · Crystal structure analysis of a basic phospholipase A2 from Trimeresurus stejnegeri venom · the same entry in another collection · chain A against A, TM-score 1.00
- Q6H3D7 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog cts-R6 (Q6H3D7) · 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 Q6H3D7
- Elsewhere: RCSB PDB 4H0S · PDBe 4H0S · UniProt Q6H3D7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.