Research workbench
Crotoxin B, the basic PLA2 from crotalus durissus terrificus.
Analyse Crotoxin B, the basic PLA2 from crotalus durissus terrificus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QOG
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2 CB2; Phospholipase A2 CB1
- EC
- 3.1.1.4
- UniProt
- P24027, P62022
- Ligands
- CA
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Phospholipase A2 CB2 (EC 3.1.1.4) | protein | 122 | 51% helix, 9% strand | P24027 |
| B, C | Phospholipase A2 CB1 (EC 3.1.1.4) | protein | 122 | 45% helix, 3% strand | P62022 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.84 | 0.85 | 111 | empty |
| 2 | 50 | 0.67 | 0.96 | 19 | empty |
| 3 | 50 | 0.65 | 0.95 | 20 | empty |
| 4 | 145 | 0.55 | 0.82 | 31 | empty |
| 5 | 145 | 0.53 | 0.81 | 30 | empty |
Interfaces
5 interfaces between chains.
- B–D · 832 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 823 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 454 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 242 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 236 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 2QOG · Crotoxin B, the basic PLA2 from Crotalus durissus terrificus. · the same entry in another collection · chain A against A, TM-score 1.00
- P62022 · AlphaFold monomer V2.0 prediction for phospholipase A2 crotoxin basic subunit cbc (P62022) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P24027 · AlphaFold monomer V2.0 prediction for phospholipase A2 crotoxin basic chain CBA2 (P24027) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P24027
- Every structure of UniProt P62022
- Elsewhere: RCSB PDB 2QOG · PDBe 2QOG · UniProt P24027 · UniProt P62022
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