Research workbench
Structure of hemoglobin from flightless bird (struthio camelus)
Analyse Structure of hemoglobin from flightless bird (struthio camelus) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A59
- Type
- protein
- Length
- 1,148 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-a; Hemoglobin subunit beta
- UniProt
- P01981, P02123
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Hemoglobin subunit alpha-a | protein | 141 | 72% helix, 0% strand | P01981 |
| B, D, F, H | Hemoglobin subunit beta | protein | 146 | 79% helix, 0% strand | P02123 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.86 | 0.87 | 94 | empty |
| 2 | 639 | 0.84 | 0.89 | 85 | HEM |
| 3 | 323 | 0.80 | 0.89 | 45 | HEM |
| 4 | 461 | 0.78 | 0.86 | 38 | empty |
| 5 | 271 | 0.75 | 0.88 | 38 | HEM |
Interfaces
14 interfaces between chains.
- C–D · 1006 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 994 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 964 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 953 Ų buried · 5 hydrogen bonds · protein-protein
- E–H · 480 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3A59 · Structure of Hemoglobin from flightless bird (Struthio camelus) · the same entry in another collection · chain G against G, TM-score 1.00
- P01981 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-a (P01981) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P02123 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P02123) · 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 P01981
- Every structure of UniProt P02123
- Elsewhere: RCSB PDB 3A59 · PDBe 3A59 · UniProt P01981 · UniProt P02123
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