Research workbench
Structure of cadmium-substituted phospholipase A2 from agkistrondon halys pallas at 2.8 ångströms resolution
Analyse Structure of cadmium-substituted phospholipase A2 from agkistrondon halys… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C1J
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P04417
- Ligands
- CD
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Basic phospholipase A2 (EC 3.1.1.4) | protein | 122 | 46% helix, 3% strand | P04417 |
Ligands and binding sites
- CD · Cadmium ion · metal · 6 copies · chains A, B, C, D
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.82 | 0.92 | 57 | BOG, CD |
| 2 | 225 | 0.78 | 0.91 | 45 | CD |
| 3 | 183 | 0.76 | 0.92 | 35 | CD |
| 4 | 133 | 0.74 | 0.93 | 33 | BOG, CD |
| 5 | 53 | 0.30 | 0.76 | 17 | empty |
Interfaces
6 interfaces between chains.
- B–C · 809 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 781 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 371 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 317 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 242 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 1C1J · Structure of cadmium-substituted phospholipase A2 from agkistrondon halys pallas at 2.8… · the same entry in another collection · chain A against A, TM-score 1.00
- P04417 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 (P04417) · 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 P04417
- Elsewhere: RCSB PDB 1C1J · PDBe 1C1J · UniProt P04417
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