Research workbench
Crystal structure of carbon monoxy hemoglobin in complex with 5HMF at 1.8 ångström
Analyse Crystal structure of carbon monoxy hemoglobin in complex with 5HMF at 1.8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UD8
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM, MW0, OXY
- Pockets
- 8 · best druggability 0.80
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 | 79% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- MW0 · (5-methylfuran-2-yl)methanol · ligand · 2 copies · chains A, C
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.80 | 0.89 | 72 | empty |
| 2 | 241 | 0.75 | 0.89 | 43 | empty |
| 3 | 222 | 0.73 | 0.88 | 28 | OXY, HEM |
| 4 | 206 | 0.73 | 0.88 | 27 | OXY, HEM |
| 5 | 200 | 0.70 | 0.86 | 25 | OXY, HEM |
Interfaces
6 interfaces between chains.
- A–B · 929 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 884 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 455 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 430 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 380 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7UD8 · Crystal structure of carbon monoxy Hemoglobin in complex with 5HMF at 1.8 Angstrom · the same entry in another collection · chain D against D, 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 0.98
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 7UD8 · PDBe 7UD8 · UniProt P69905 · UniProt P68871
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