Research workbench
X-ray structure of carbonmonoxy hemoglobin of eleginops maclovinus
Analyse X-ray structure of carbonmonoxy hemoglobin of eleginops maclovinus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ESA
- Type
- protein
- Length
- 573 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha chain; Hemoglobin beta chain
- Ligands
- HEM, ACE, CMO
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin alpha chain | protein | 142 | 76% helix, 0% strand | — |
| B | Hemoglobin beta chain | protein | 144 | 81% helix, 0% strand | — |
| D | Hemoglobin beta chain | protein | 145 | 77% helix, 0% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- ACE · Acetyl group · ligand · 2 copies · chains A, C
- CMO · Carbon monoxide · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.85 | 0.86 | 108 | ACE |
| 2 | 266 | 0.76 | 0.88 | 32 | CMO, HEM |
| 3 | 269 | 0.75 | 0.87 | 32 | CMO, HEM |
| 4 | 249 | 0.74 | 0.88 | 29 | CMO, HEM |
| 5 | 224 | 0.74 | 0.88 | 28 | CMO, HEM |
Interfaces
6 interfaces between chains.
- C–D · 860 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 852 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 582 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 566 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 466 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4ESA · X-ray structure of carbonmonoxy hemoglobin of Eleginops maclovinus · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4ESA · PDBe 4ESA
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