Research workbench
Staphylococcus aureus isda neat domain Y166A variant in complex with heme
Analyse Staphylococcus aureus isda neat domain Y166A variant in complex with heme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QZN
- Type
- protein
- Length
- 363 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-regulated surface determinant protein a
- UniProt
- Q7A655
- Ligands
- HEM, SO4
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Iron-regulated surface determinant protein a | protein | 121 | 9% helix, 59% strand | Q7A655 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.53 | 0.83 | 18 | HEM |
| 2 | 84 | 0.53 | 0.84 | 17 | HEM |
| 3 | 100 | 0.52 | 0.82 | 16 | HEM |
| 4 | 167 | 0.49 | 0.77 | 26 | empty |
| 5 | 62 | 0.32 | 0.76 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 708 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 449 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3QZN · Staphylococcus aureus IsdA NEAT domain Y166A variant in complex with heme · the same entry in another collection · chain A against A, TM-score 1.00
- Q7A655 · AlphaFold monomer V2.0 prediction for iron-regulated surface determinant protein a… · a predicted model of the same protein · chain A 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 Q7A655
- Elsewhere: RCSB PDB 3QZN · PDBe 3QZN · UniProt Q7A655
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