Research workbench
R-state form of chicken hemoglobin D
Analyse R-state form of chicken hemoglobin D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HBR
- Type
- protein
- Length
- 570 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (hemoglobin D)
- UniProt
- P02001, P02112
- Ligands
- HEM
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (hemoglobin D) | protein | 141 | 75% helix, 0% strand | P02001 |
| B | Protein (hemoglobin D) | protein | 143 | 80% helix, 0% strand | P02112 |
| C | Protein (hemoglobin D) | protein | 140 | 76% helix, 0% strand | P02001 |
| D | Protein (hemoglobin D) | protein | 146 | 80% helix, 0% strand | P02112 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.83 | 0.84 | 109 | empty |
| 2 | 238 | 0.73 | 0.87 | 27 | HEM |
| 3 | 240 | 0.73 | 0.87 | 28 | HEM |
| 4 | 210 | 0.71 | 0.86 | 25 | HEM |
| 5 | 214 | 0.70 | 0.86 | 25 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 962 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 960 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 475 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 465 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 132 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1HBR · R-state form of chicken hemoglobin D · the same entry in another collection · chain D against D, TM-score 1.00
- P02112 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P02112) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P02001 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-D (P02001) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P02001
- Every structure of UniProt P02112
- Elsewhere: RCSB PDB 1HBR · PDBe 1HBR · UniProt P02001 · UniProt P02112
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