Research workbench
Crystal structure of trematomus bernacchii hemoglobin in a partial hemichrome state
Analyse Crystal structure of trematomus bernacchii hemoglobin in a partial hemichrome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PEG
- Type
- protein
- Length
- 283 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P80043, P80044
- Ligands
- HEM, ACE
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin subunit alpha | protein | 142 | 78% helix, 0% strand | P80043 |
| B | Hemoglobin subunit beta | protein | 141 | 74% helix, 0% strand | P80044 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- ACE · Acetyl group · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.73 | 0.89 | 26 | HEM |
| 2 | 219 | 0.72 | 0.87 | 27 | HEM |
| 3 | 170 | 0.44 | 0.75 | 26 | empty |
| 4 | 61 | 0.33 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 853 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2PEG · Crystal structure of Trematomus bernacchii hemoglobin in a partial hemichrome state · the same entry in another collection · chain A against A, TM-score 1.00
- P80043 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P80043) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P80044 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P80044) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P80043
- Every structure of UniProt P80044
- Elsewhere: RCSB PDB 2PEG · PDBe 2PEG · UniProt P80043 · UniProt P80044
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