Research workbench
Met-perch hemoglobin at 1.9A
Analyse Met-perch hemoglobin at 1.9A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XQ5
- Type
- protein
- Length
- 576 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha-1 chain; Hemoglobin beta-2 chain
- UniProt
- A8HTG8
- Ligands
- HEM, ACE
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin alpha-1 chain | protein | 142 | 80% helix, 0% strand | A8HTG8 |
| B, D | Hemoglobin beta-2 chain | protein | 146 | 76% helix, 0% strand | — |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.84 | 0.85 | 113 | ACE |
| 2 | 224 | 0.73 | 0.88 | 27 | HEM |
| 3 | 232 | 0.72 | 0.87 | 30 | HEM |
| 4 | 218 | 0.72 | 0.87 | 28 | HEM |
| 5 | 235 | 0.72 | 0.87 | 32 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 902 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 877 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 552 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 549 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 478 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1XQ5 · Met-Perch Hemoglobin at 1.9A · the same entry in another collection · chain A against A, 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 A8HTG8
- Elsewhere: RCSB PDB 1XQ5 · PDBe 1XQ5 · UniProt A8HTG8
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