Research workbench
Structure of human haptoglobin-hemoglobin bound to S. aureus isdh
Analyse Structure of human haptoglobin-hemoglobin bound to S. aureus isdh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TB2
- Type
- protein
- Length
- 1,209 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta; Haptoglobin; Cell wall surface anchor…
- UniProt
- P69905, P68871, P00738, A0A0E8IWL6
- Ligands
- HEM
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin subunit alpha | protein | 141 | 78% helix, 0% strand | P69905 |
| B | Hemoglobin subunit beta | protein | 146 | 75% helix, 0% strand | P68871 |
| C | Haptoglobin | protein | 256 | 14% helix, 30% strand | P00738 |
| D, E | Cell wall surface anchor family protein | protein | 333 | 22% helix, 42% strand | A0A0E8IWL6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.81 | 0.81 | 82 | HEM |
| 2 | 929 | 0.76 | 0.79 | 69 | HEM |
| 3 | 711 | 0.75 | 0.80 | 80 | empty |
| 4 | 221 | 0.67 | 0.84 | 33 | empty |
| 5 | 252 | 0.58 | 0.78 | 27 | empty |
Interfaces
8 interfaces between chains.
- B–E · 1221 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 951 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 842 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 762 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 731 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6TB2 · Structure of human haptoglobin-hemoglobin bound to S. aureus IsdH · the same entry in another collection · chain B against B, TM-score 1.00
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P00738 · AlphaFold monomer V2.0 prediction for haptoglobin (P00738) · 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 P00738
- Every structure of UniProt A0A0E8IWL6
- Elsewhere: RCSB PDB 6TB2 · PDBe 6TB2 · UniProt P69905 · UniProt P68871 · UniProt P00738 · UniProt A0A0E8IWL6
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