Research workbench
X ray crystal structure of rabbit hemoglobin (oxy form) at 2.0 ångström resolution
Analyse X ray crystal structure of rabbit hemoglobin (oxy form) at 2.0 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RAO
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-1/2; Hemoglobin subunit beta-1/2
- UniProt
- P01948, P02057
- Ligands
- HEM, OXY
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha-1/2 | protein | 141 | 77% helix, 0% strand | P01948 |
| B, D | Hemoglobin subunit beta-1/2 | protein | 146 | 77% helix, 0% strand | P02057 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.86 | 0.87 | 126 | empty |
| 2 | 256 | 0.73 | 0.86 | 29 | HEM, OXY |
| 3 | 258 | 0.72 | 0.86 | 28 | OXY, HEM |
| 4 | 193 | 0.71 | 0.87 | 24 | HEM, OXY |
| 5 | 223 | 0.70 | 0.85 | 26 | OXY, HEM |
Interfaces
6 interfaces between chains.
- A–B · 939 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 937 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 485 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 483 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 381 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2RAO · X ray crystal structure of rabbit hemoglobin (oxy form) at 2.0 angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P02057 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-1/2 (P02057) · a predicted model of the same protein · chain B against A, TM-score 0.97
- P01948 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-1/2 (P01948) · 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 P01948
- Every structure of UniProt P02057
- Elsewhere: RCSB PDB 2RAO · PDBe 2RAO · UniProt P01948 · UniProt P02057
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