Research workbench
Crystal structure determination of porcine hemoglobin at 1.8A resolution
Analyse Crystal structure determination of porcine hemoglobin at 1.8A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QPW
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Porcine hemoglobin (alpha subunit); Porcine hemoglobin (beta subunit)
- UniProt
- P01965, P02067
- Ligands
- HEM, OXY
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Porcine hemoglobin (alpha subunit) | protein | 141 | 77% helix, 0% strand | P01965 |
| B, D | Porcine hemoglobin (beta subunit) | protein | 146 | 79% helix, 0% strand | P02067 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 2 copies · chains B, 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 | 374 | 0.80 | 0.89 | 55 | empty |
| 2 | 389 | 0.80 | 0.89 | 49 | empty |
| 3 | 262 | 0.75 | 0.87 | 29 | HEM |
| 4 | 268 | 0.74 | 0.87 | 29 | HEM, OXY |
| 5 | 261 | 0.73 | 0.86 | 28 | HEM, OXY |
Interfaces
6 interfaces between chains.
- C–D · 944 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 870 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 664 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 559 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 272 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1QPW · Crystal structure determination of porcine hemoglobin at 1.8A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P02067 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P02067) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P01965 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P01965) · a predicted model of the same protein · chain A 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 P01965
- Every structure of UniProt P02067
- Elsewhere: RCSB PDB 1QPW · PDBe 1QPW · UniProt P01965 · UniProt P02067
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