Research workbench
Hemoglobin thionville: an alpha-chain variant with a substitution of a glutamate for valine at na-1 and having an acetylated methionine NH2 terminus
Analyse Hemoglobin thionville: an alpha-chain variant with a substitution of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BAB
- Type
- protein
- Length
- 576 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin thionville (deoxy) (alpha chain); Hemoglobin thionville (deoxy) (beta chain)
- UniProt
- P69905, P68871
- Ligands
- HEM, ACE, SO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin thionville (deoxy) (alpha chain) | protein | 142 | 78% helix, 0% strand | P69905 |
| B, D | Hemoglobin thionville (deoxy) (beta chain) | protein | 146 | 81% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- ACE · Acetyl group · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.82 | 0.84 | 74 | empty |
| 2 | 220 | 0.74 | 0.88 | 31 | HEM |
| 3 | 211 | 0.73 | 0.88 | 28 | HEM |
| 4 | 264 | 0.72 | 0.86 | 35 | HEM |
| 5 | 261 | 0.71 | 0.85 | 31 | HEM |
Interfaces
5 interfaces between chains.
- A–B · 873 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 871 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 724 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 718 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1BAB · Hemoglobin thionville: an alpha-chain variant with a substitution of a glutamate for… · the same entry in another collection · chain C against C, TM-score 1.00
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
- Elsewhere: RCSB PDB 1BAB · PDBe 1BAB · UniProt P69905 · UniProt P68871
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