Research workbench
Hemoglobin structure from serial crystallography with a 3D-printed nozzle.
Analyse Hemoglobin structure from serial crystallography with a 3D-printed nozzle. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R2O
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P01958, P02062
- Ligands
- HEM, NA, CL
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 77% helix, 0% strand | P01958 |
| B, D | Hemoglobin subunit beta | protein | 145 | 79% helix, 0% strand | P02062 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · chains 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 | 1070 | 0.86 | 0.87 | 103 | NA |
| 2 | 251 | 0.74 | 0.87 | 30 | HEM |
| 3 | 271 | 0.73 | 0.86 | 32 | HEM |
| 4 | 284 | 0.73 | 0.86 | 25 | empty |
| 5 | 208 | 0.71 | 0.87 | 24 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 953 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 927 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 550 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 518 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 366 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6R2O · Hemoglobin structure from serial crystallography with a 3D-printed nozzle. · the same entry in another collection · chain A against A, TM-score 1.00
- P02062 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P02062) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P01958 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P01958) · 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 P01958
- Every structure of UniProt P02062
- Elsewhere: RCSB PDB 6R2O · PDBe 6R2O · UniProt P01958 · UniProt P02062
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