Research workbench
Deoxy RHB1.1 (recombinant hemoglobin)
Analyse Deoxy RHB1.1 (recombinant hemoglobin) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ABW
- Type
- protein
- Length
- 577 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin-based blood substitute
- UniProt
- P69905, P68871
- Ligands
- HEM, MET, LEU
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin-based blood substitute | protein | 285 | 77% helix, 0% strand | P69905 |
| B, D | Hemoglobin-based blood substitute | protein | 146 | 79% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, D
- MET · Methionine · ligand · chains A
- LEU · Leucine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.82 | 0.83 | 80 | empty |
| 2 | 256 | 0.75 | 0.87 | 29 | HEM |
| 3 | 214 | 0.73 | 0.87 | 27 | HEM |
| 4 | 203 | 0.71 | 0.87 | 27 | HEM |
| 5 | 241 | 0.70 | 0.85 | 30 | HEM |
Interfaces
2 interfaces between chains.
- A–B · 1541 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1535 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 covalent (covalent ligand).
Compared structures
- 1ABW · Deoxy RHB1.1 (recombinant hemoglobin) · the same entry in another collection · chain A against A, TM-score 1.00
- P68871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P68871) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain A against A, TM-score 0.50
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 P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 1ABW · PDBe 1ABW · UniProt P69905 · UniProt P68871
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