Research workbench
Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin a (SPEA1): implications for MHC class II recognition.
Analyse Structural features of a zinc-binding site in the superantigen streptococcal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HA5
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptococcal pyogenic exotoxin A1
- UniProt
- P08095
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Streptococcal pyogenic exotoxin A1 | protein | 218 | 18% helix, 39% strand | P08095 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.88 | 0.90 | 112 | empty |
| 2 | 238 | 0.59 | 0.79 | 22 | empty |
| 3 | 99 | 0.54 | 0.84 | 20 | empty |
| 4 | 64 | 0.51 | 0.86 | 14 | empty |
| 5 | 90 | 0.51 | 0.83 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 806 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 748 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 672 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 667 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 245 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1HA5 · Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic… · the same entry in another collection · chain A against A, TM-score 1.00
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 P08095
- Elsewhere: RCSB PDB 1HA5 · PDBe 1HA5 · UniProt P08095
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