Research workbench
Crystal structure at acidic pH of the ferric form of the root effect hemoglobin from trematomus bernacchii.
Analyse Crystal structure at acidic pH of the ferric form of the root effect hemoglobin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GQG
- Type
- protein
- Length
- 576 residues
- Chains
- 4
- 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
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 142 | 75% helix, 0% strand | P80043 |
| B, D | Hemoglobin subunit beta | protein | 146 | 74% helix, 0% strand | P80044 |
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
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.82 | 0.83 | 79 | ACE |
| 2 | 212 | 0.73 | 0.88 | 28 | HEM |
| 3 | 231 | 0.72 | 0.87 | 30 | HEM |
| 4 | 231 | 0.72 | 0.86 | 28 | HEM |
| 5 | 210 | 0.71 | 0.87 | 27 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 834 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 796 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 740 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 675 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 502 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3GQG · Crystal structure at acidic pH of the ferric form of the Root effect hemoglobin from… · 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 0.99
- P80044 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P80044) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 3GQG · PDBe 3GQG · UniProt P80043 · UniProt P80044
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