Research workbench
Crystal structure of ecarpholin S complexed with suramin
Analyse Crystal structure of ecarpholin S complexed with suramin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BJW
- Type
- protein
- Length
- 976 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P48650
- Ligands
- SVR
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Phospholipase A2 (EC 3.1.1.4) | protein | 122 | 47% helix, 8% strand | P48650 |
Ligands and binding sites
- SVR · 8,8'-[carbonylbis[imino-3,1-phenylenecarbonylimino(4-methyl-3,1-phenylene)carbonylimino]]bis-1,3,5-naphthalenetrisulfonic acid · ligand · 12 copies · chains A, E, G, H, B, F, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.78 | 0.79 | 85 | SVR |
| 2 | 948 | 0.78 | 0.80 | 83 | SVR |
| 3 | 641 | 0.76 | 0.82 | 66 | SVR |
| 4 | 512 | 0.74 | 0.82 | 55 | SVR |
| 5 | 252 | 0.65 | 0.82 | 25 | empty |
Interfaces
16 interfaces between chains.
- C–D · 680 Ų buried · 11 hydrogen bonds · protein-protein
- A–G · 676 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 374 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 373 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 356 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 3BJW · Crystal Structure of ecarpholin S complexed with suramin · the same entry in another collection · chain H against H, TM-score 1.00
- P48650 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog ecarpholin S (P48650) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P48650
- Elsewhere: RCSB PDB 3BJW · PDBe 3BJW · UniProt P48650
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