Research workbench
Crystal structure isda neat domain from staphylococcus aureus with heme bound
Analyse Crystal structure isda neat domain from staphylococcus aureus with heme bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ITF
- Type
- protein
- Length
- 486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-regulated surface determinant protein a
- UniProt
- Q7A152
- Ligands
- HEM
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 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, 60% strand | Q7A152 |
| D | Iron-regulated surface determinant protein a | protein | 123 | 9% helix, 59% strand | Q7A152 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.78 | 0.80 | 76 | HEM |
| 2 | 616 | 0.73 | 0.80 | 61 | HEM |
| 3 | 268 | 0.57 | 0.78 | 35 | empty |
Interfaces
5 interfaces between chains.
- C–D · 438 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 409 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 295 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 229 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 222 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2ITF · Crystal structure IsdA NEAT domain from Staphylococcus aureus with heme bound · the same entry in another collection · chain A against A, TM-score 1.00
- Q7A152 · AlphaFold monomer V2.0 prediction for iron-regulated surface determinant protein a… · a predicted model of the same protein · chain D 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 Q7A152
- Elsewhere: RCSB PDB 2ITF · PDBe 2ITF · UniProt Q7A152
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