Research workbench
Deoxy RHB1.2 (recombinant hemoglobin)
Analyse Deoxy RHB1.2 (recombinant hemoglobin) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C7D
- Type
- protein
- Length
- 576 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (deoxyhemoglobin (alpha chain)); Protein (deoxyhemoglobin (beta chain))
- UniProt
- P69905, P68871
- Ligands
- HEM
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (deoxyhemoglobin (alpha chain)) | protein | 284 | 76% helix, 0% strand | P69905 |
| B, D | Protein (deoxyhemoglobin (beta chain)) | protein | 146 | 82% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.79 | 0.81 | 87 | empty |
| 2 | 265 | 0.74 | 0.87 | 30 | HEM |
| 3 | 223 | 0.74 | 0.88 | 29 | HEM |
| 4 | 222 | 0.72 | 0.87 | 26 | HEM |
| 5 | 259 | 0.71 | 0.85 | 29 | HEM |
Interfaces
2 interfaces between chains.
- A–D · 1540 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1537 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1C7D · Deoxy RHB1.2 (recombinant hemoglobin) · the same entry in another collection · chain A against A, TM-score 1.00
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 1C7D · PDBe 1C7D · UniProt P69905 · UniProt P68871
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