Research workbench
Structure determination of aquomet porcine hemoglobin at 2.8 ångström resolution
Analyse Structure determination of aquomet porcine hemoglobin at 2.8 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PGH
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin (aquo met) (alpha chain); Hemoglobin (aquo met) (beta chain)
- UniProt
- P01965, P02067
- Ligands
- HEM
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin (aquo met) (alpha chain) | protein | 141 | 74% helix, 0% strand | P01965 |
| B, D | Hemoglobin (aquo met) (beta chain) | protein | 146 | 73% helix, 0% strand | P02067 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, 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 | 1044 | 0.86 | 0.86 | 93 | empty |
| 2 | 285 | 0.76 | 0.87 | 28 | HEM |
| 3 | 268 | 0.73 | 0.86 | 32 | HEM |
| 4 | 237 | 0.72 | 0.87 | 29 | HEM |
| 5 | 250 | 0.71 | 0.86 | 25 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 937 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 860 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 619 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 546 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 330 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2PGH · Structure determination of aquomet porcine hemoglobin at 2.8 ångström 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 2PGH · PDBe 2PGH · UniProt P01965 · UniProt P02067
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