Research workbench
Crystal structure of dog (canis familiaris) hemoglobin
Analyse Crystal structure of dog (canis familiaris) hemoglobin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GOU
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P60529, P60524
- Ligands
- HEM
- Pockets
- 9 · 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 | 141 | 74% helix, 0% strand | P60529 |
| B, D | Hemoglobin subunit beta | protein | 146 | 75% helix, 0% strand | P60524 |
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
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.82 | 0.89 | 58 | empty |
| 2 | 354 | 0.79 | 0.89 | 41 | empty |
| 3 | 233 | 0.77 | 0.90 | 29 | HEM |
| 4 | 252 | 0.75 | 0.87 | 28 | HEM |
| 5 | 212 | 0.71 | 0.87 | 31 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 944 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 912 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 547 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 525 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 244 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3GOU · Crystal structure of dog (Canis familiaris) hemoglobin · the same entry in another collection · chain A against A, TM-score 1.00
- P60529 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P60529) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P60524 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P60524) · a predicted model of the same protein · chain B 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 P60529
- Every structure of UniProt P60524
- Elsewhere: RCSB PDB 3GOU · PDBe 3GOU · UniProt P60529 · UniProt P60524
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