Research workbench
Crystal structure determination of duck (anas platyrhynchos) hemoglobin at 2.1 ångström resolution
Analyse Crystal structure determination of duck (anas platyrhynchos) hemoglobin at 2.1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EOK
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-a; Hemoglobin subunit beta
- UniProt
- P01986, P02114
- Ligands
- HEM
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin subunit alpha-a | protein | 141 | 77% helix, 0% strand | P01986 |
| B | Hemoglobin subunit beta | protein | 146 | 83% helix, 0% strand | P02114 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.73 | 0.87 | 33 | HEM |
| 2 | 231 | 0.71 | 0.86 | 30 | HEM |
| 3 | 98 | 0.51 | 0.83 | 22 | empty |
| 4 | 77 | 0.37 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1007 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3EOK · Crystal structure determination of duck (Anas platyrhynchos) hemoglobin at 2.1 Angstrom… · the same entry in another collection · chain A against A, TM-score 1.00
- P02114 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P02114) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P01986 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-a (P01986) · a predicted model of the same protein · chain A 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 P01986
- Every structure of UniProt P02114
- Elsewhere: RCSB PDB 3EOK · PDBe 3EOK · UniProt P01986 · UniProt P02114
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