Research workbench
Crystal structure of carbonmonoxy horse hemoglobin complexed with L35
Analyse Crystal structure of carbonmonoxy horse hemoglobin complexed with L35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D5X
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha subunit; Hemoglobin beta subunit
- UniProt
- P01958, P02062
- Ligands
- HEM, L35, CMO
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin alpha subunit | protein | 141 | 74% helix, 0% strand | P01958 |
| B | Hemoglobin beta subunit | protein | 146 | 82% helix, 0% strand | P02062 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- L35 · 2-[4-({[(3,5-dichlorophenyl)amino]carbonyl}amino)phenoxy]-2-methylpropanoic acid · ligand · 2 copies · chains A, B
- CMO · Carbon monoxide · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.71 | 0.87 | 26 | HEM, CMO |
| 2 | 177 | 0.70 | 0.87 | 24 | HEM, CMO |
| 3 | 222 | 0.54 | 0.77 | 33 | L35 |
| 4 | 54 | 0.35 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 906 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2D5X · Crystal structure of carbonmonoxy horse hemoglobin complexed with L35 · the same entry in another collection · chain A against A, TM-score 1.00
- P01958 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P01958) · a predicted model of the same protein · chain A against A, TM-score 0.98
- 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
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 2D5X · PDBe 2D5X · UniProt P01958 · UniProt P02062
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