Research workbench
Human methemoglobin in complex with the second and third neat domains of ISDH(F365Y/A369F/Y642A) from staphylococcus aureus
Analyse Human methemoglobin in complex with the second and third neat domains of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XS0
- Type
- protein
- Length
- 603 residues
- Chains
- 3
- 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, Q2FG07
- Ligands
- HEM, CL, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin subunit alpha | protein | 141 | 79% helix, 0% strand | P69905 |
| B | Hemoglobin subunit beta | protein | 146 | 78% helix, 0% strand | P68871 |
| C | Iron-regulated surface determinant protein H | protein | 316 | 25% helix, 41% strand | Q2FG07 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C, B
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains C
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 | 1152 | 0.81 | 0.82 | 89 | HEM, CL |
| 2 | 188 | 0.69 | 0.86 | 24 | HEM |
| 3 | 209 | 0.51 | 0.76 | 35 | CL |
| 4 | 192 | 0.47 | 0.75 | 35 | empty |
| 5 | 95 | 0.43 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1434 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 865 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 96 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4XS0 · Human methemoglobin in complex with the second and third NEAT domains of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2FG07 · 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 0.98
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 Q2FG07
- Elsewhere: RCSB PDB 4XS0 · PDBe 4XS0 · UniProt P69905 · UniProt P68871 · UniProt Q2FG07
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