Research workbench
Crystal structure of crotoxin
Analyse Crystal structure of crotoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R0L
- Type
- protein
- Length
- 193 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crotoxin chain a; Crotoxin chain B; Crotoxin chain C; Phospholipase A2 cb
- EC
- 3.1.1.4
- UniProt
- P08878, P62022
- Ligands
- NA, MN, CL
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Crotoxin chain a | protein | 33 | 48% helix, 9% strand | P08878 |
| B | Crotoxin chain B | protein | 32 | 66% helix, 0% strand | P08878 |
| C | Crotoxin chain C | protein | 6 | 0% helix, 0% strand | P08878 |
| D | Phospholipase A2 cb (EC 3.1.1.4) | protein | 122 | 48% helix, 7% strand | P62022 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains D
- MN · Manganese (II) ion · metal · chains D
- CL · Chloride ion · ion · chains B, D
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.69 | 0.86 | 32 | ACT |
| 2 | 70 | 0.38 | 0.78 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–D · 646 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 579 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 444 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 298 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 3R0L · Crystal structure of crotoxin · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.97
- P08878 · AlphaFold monomer V2.0 prediction for phospholipase A2 homolog crotoxin acid subunit ca… · a predicted model of the same protein · chain B against A, TM-score 0.72
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 P08878
- Every structure of UniProt P62022
- Elsewhere: RCSB PDB 3R0L · PDBe 3R0L · UniProt P08878 · UniProt P62022
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