MolNFT v1 · #78279 · protein
Human alpha-haemoglobin complexed with the first neat domain of isdh from staphylococcus aureus
3S48 · Iron-regulated surface determinant protein H: “Human alpha-haemoglobin complexed with the first neat domain of isdh from staphylococcus aureus”. X-ray diffraction, 1 ligand (HEM), 10 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 3S48
- Type
- protein
- Length
- 562 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-regulated surface determinant protein H; Hemoglobin subunit alpha
- UniProt
- Q6G8J7, P69905
- Ligands
- HEM
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron-regulated surface determinant protein H | protein | 143 | 9% helix, 43% strand | Q6G8J7 |
| D | Hemoglobin subunit alpha | protein | 140 | 79% helix, 0% strand | P69905 |
| B | Iron-regulated surface determinant protein H | protein | 141 | 7% helix, 38% strand | Q6G8J7 |
| C | Hemoglobin subunit alpha | protein | 138 | 78% helix, 0% strand | P69905 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.75 | 0.87 | 40 | HEM |
| 2 | 262 | 0.74 | 0.87 | 31 | HEM |
| 3 | 77 | 0.70 | 0.94 | 33 | empty |
| 4 | 263 | 0.58 | 0.78 | 37 | empty |
| 5 | 255 | 0.57 | 0.78 | 36 | empty |
Interfaces
3 interfaces between chains.
- D–C · 749 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 642 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 633 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3S48 · Human Alpha-Haemoglobin Complexed with the First NEAT Domain of IsdH from Staphylococcus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6G8J7 · AlphaFold monomer V2.0 prediction for iron-regulated surface determinant protein H… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q6G8J7
- Every structure of UniProt P69905
- Elsewhere: RCSB PDB 3S48 · PDBe 3S48 · UniProt Q6G8J7 · UniProt P69905
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