Research workbench
Crystal structure of ferrocyanide bound human hemoglobin A2 at 1.88A resolution
Analyse Crystal structure of ferrocyanide bound human hemoglobin A2 at 1.88A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SHR
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha chain; Hemoglobin delta chain
- UniProt
- P69905, P02042
- Ligands
- HEM, FE, CYN
- Pockets
- 7 · 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 alpha chain | protein | 141 | 76% helix, 0% strand | P69905 |
| B, D | Hemoglobin delta chain | protein | 146 | 77% helix, 0% strand | P02042 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 3 copies · chains A, B, D
- CYN · Cyanide ion · ion · 10 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.86 | 0.87 | 123 | empty |
| 2 | 253 | 0.76 | 0.88 | 33 | CYN, HEM |
| 3 | 255 | 0.74 | 0.87 | 29 | CYN, HEM |
| 4 | 194 | 0.69 | 0.86 | 25 | CYN, HEM |
| 5 | 205 | 0.69 | 0.85 | 25 | CYN, HEM |
Interfaces
6 interfaces between chains.
- C–D · 946 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 921 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 503 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 499 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 412 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1SHR · Crystal structure of ferrocyanide bound human hemoglobin A2 at 1.88A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P02042 · AlphaFold monomer V2.0 prediction for hemoglobin subunit delta (P02042) · a predicted model of the same protein · chain B 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 P69905
- Every structure of UniProt P02042
- Elsewhere: RCSB PDB 1SHR · PDBe 1SHR · UniProt P69905 · UniProt P02042
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