Research workbench
Crystal structure of human methaemoglobin complexed with the first neat domain of isdh from staphylococcus aureus
Analyse Crystal structure of human methaemoglobin complexed with the first neat domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SZK
- Type
- protein
- Length
- 830 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta; Iron-regulated surface determinant…
- UniProt
- P69905, P68871, Q8NW39
- Ligands
- HEM
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | Hemoglobin subunit alpha | protein | 140 | 79% helix, 0% strand | P69905 |
| B | Hemoglobin subunit beta | protein | 142 | 80% helix, 0% strand | P68871 |
| E | Hemoglobin subunit beta | protein | 123 | 78% helix, 0% strand | P68871 |
| F | Iron-regulated surface determinant protein H | protein | 141 | 9% helix, 42% strand | Q8NW39 |
| C | Iron-regulated surface determinant protein H | protein | 144 | 7% helix, 47% strand | Q8NW39 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains D, B, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.72 | 0.87 | 27 | HEM |
| 2 | 210 | 0.71 | 0.86 | 27 | HEM |
| 3 | 199 | 0.69 | 0.86 | 25 | HEM |
| 4 | 255 | 0.66 | 0.82 | 28 | HEM |
| 5 | 242 | 0.55 | 0.77 | 49 | empty |
Interfaces
4 interfaces between chains.
- B–A · 887 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 886 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 657 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 648 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3SZK · Crystal Structure of Human metHaemoglobin Complexed with the First NEAT Domain of IsdH… · the same entry in another collection · chain C against C, TM-score 1.00
- Q8NW39 · AlphaFold monomer V2.0 prediction for iron-regulated surface determinant protein H… · a predicted model of the same protein · chain C 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 P69905
- Every structure of UniProt P68871
- Every structure of UniProt Q8NW39
- Elsewhere: RCSB PDB 3SZK · PDBe 3SZK · UniProt P69905 · UniProt P68871 · UniProt Q8NW39
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