Research workbench
Crystal structure of a zinc containing dimer of phospholipase A2 from the venom of indian cobra (naja naja sagittifera)
Analyse Crystal structure of a zinc containing dimer of phospholipase A2 from the venom… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MH2
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P60043, P60044
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 (EC 3.1.1.4) | protein | 119 | 47% helix, 9% strand | P60043 |
| B | Phospholipase A2 (EC 3.1.1.4) | protein | 119 | 47% helix, 8% strand | P60044 |
Ligands and binding sites
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 | 296 | 0.73 | 0.86 | 35 | empty |
| 2 | 404 | 0.72 | 0.83 | 37 | ACY |
Interfaces
1 interface between chains.
- A–B · 1054 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1MH2 · Crystal Structure of a Zinc Containing Dimer of Phospholipase A2 from the Venom of Indian… · the same entry in another collection · chain A against A, TM-score 1.00
- P60043 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 1 (P60043) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P60044 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 2 (P60044) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P60043
- Every structure of UniProt P60044
- Elsewhere: RCSB PDB 1MH2 · PDBe 1MH2 · UniProt P60043 · UniProt P60044
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