Research workbench
The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group a streptococcus protein pam
Analyse The X-ray crystallographic structure of the angiogenesis inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DOI
- Type
- protein
- Length
- 380 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiostatin; Plasminogen-binding group a streptococcal M-like protein pam
- EC
- 3.4.21.7
- UniProt
- P00747, P49054
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Angiostatin (EC 3.4.21.7) | protein | 168 | 2% helix, 18% strand | P00747 |
| C | Plasminogen-binding group a streptococcal M-like protein pam | protein | 24 | 75% helix, 0% strand | P49054 |
| A | Angiostatin (EC 3.4.21.7) | protein | 164 | 0% helix, 16% strand | P00747 |
| B | Plasminogen-binding group a streptococcal M-like protein pam | protein | 24 | 83% helix, 0% strand | P49054 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 203 | 0.48 | 0.75 | 34 | empty |
| 2 | 171 | 0.42 | 0.74 | 24 | empty |
| 3 | 69 | 0.30 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- X–A · 890 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 594 Ų buried · 16 hydrogen bonds · protein-protein
- X–C · 535 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 2DOI · The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to… · the same entry in another collection · chain B against B, TM-score 1.00
- P49054 · AlphaFold monomer V2.0 prediction for plasminogen-binding group a streptococcal M-like… · a predicted model of the same protein · chain B against A, TM-score 0.76
- P00747 · AlphaFold monomer V2.0 prediction for plasminogen (P00747) · a predicted model of the same protein · chain A against A, TM-score 0.71
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 P00747
- Every structure of UniProt P49054
- Elsewhere: RCSB PDB 2DOI · PDBe 2DOI · UniProt P00747 · UniProt P49054
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