MolNFT v1 · #71622 · protein
Crystal structure determination of japanese quail (coturnix coturnix japonica) hemoglobin at 2.76 ångström resolution
3MJP · Hemoglobin subunit alpha-a: “Crystal structure determination of japanese quail (coturnix coturnix japonica) hemoglobin at 2.76 ångström…”. X-ray diffraction, 2 ligands (HEM, OXY), 9 pockets (best druggability 0.83). MolNFT v1 #71622…
- PDB
- 3MJP
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-a; Hemoglobin subunit beta
- UniProt
- P24589, P30893
- Ligands
- HEM, OXY
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 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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