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Crystal structure of monocarboxylated hemoglobin from the sub- antarctic fish eleginops maclovinus
Analyse Crystal structure of monocarboxylated hemoglobin from the sub- antarctic fish… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RP5
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha 1; Hemoglobin subunit beta-1
- UniProt
- K7N5M5, K7N5M6
- Ligands
- HEM, ACE, DTN, SO4, CMO
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin subunit alpha 1 | protein | 142 | 80% helix, 0% strand | K7N5M5 |
| B | Hemoglobin subunit beta-1 | protein | 144 | 79% helix, 0% strand | K7N5M6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- ACE · Acetyl group · ligand · chains A
- DTN · Dithionite · ligand · chains A, B
- SO4 · Sulfate ion · ion · 4 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.73 | 0.86 | 28 | CMO, HEM |
| 2 | 228 | 0.72 | 0.87 | 28 | CMO, HEM |
| 3 | 194 | 0.48 | 0.75 | 32 | empty |
| 4 | 59 | 0.32 | 0.76 | 16 | empty |
| 5 | 60 | 0.30 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 831 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6RP5 · Crystal structure of monocarboxylated hemoglobin from the sub-Antarctic fish Eleginops… · the same entry in another collection · chain A against A, TM-score 1.00
- K7N5M6 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-1 (K7N5M6) · a predicted model of the same protein · chain B against A, TM-score 0.97
- K7N5M5 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha 1 (K7N5M5) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 K7N5M5
- Every structure of UniProt K7N5M6
- Elsewhere: RCSB PDB 6RP5 · PDBe 6RP5 · UniProt K7N5M5 · UniProt K7N5M6
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