Research workbench
Crystal structure determination of Japanese quail (Coturnix coturnix japonica) hemoglobin at 2.76 Angstrom resolution
Analyse Crystal structure determination of Japanese quail (Coturnix coturnix japonica)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MJP
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.76
- Source
- Coturnix japonica
- Molecule
- Hemoglobin subunit alpha-A; Hemoglobin subunit beta
- UniProt
- P24589, P30893
- Ligands
- HEM, OXY
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.76 · 2 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha-A | protein | 141 | 66% helix, 0% strand | P24589 |
| B, D | Hemoglobin subunit beta | protein | 146 | 71% helix, 0% strand | P30893 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.83 | 0.90 | 56 | empty |
| 2 | 305 | 0.78 | 0.89 | 47 | empty |
| 3 | 306 | 0.75 | 0.86 | 28 | HEM, OXY |
| 4 | 237 | 0.73 | 0.87 | 30 | HEM |
| 5 | 315 | 0.73 | 0.84 | 28 | HEM, OXY |
Interfaces
6 interfaces between chains.
- A–B · 990 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 988 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 471 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 470 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 281 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3MJP · Crystal structure determination of japanese quail (coturnix coturnix japonica) hemoglobin… · the same entry in another collection · chain A against A, TM-score 1.00
- P30893 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P30893) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P24589 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-a (P24589) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P24589
- Every structure of UniProt P30893
- Elsewhere: RCSB PDB 3MJP · PDBe 3MJP · UniProt P24589 · UniProt P30893
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