MolNFT v1 · #59131 · protein
Crystal structure of trout hemoglobin at 1.35 ångström resolution
3BOM · Hemoglobin subunit alpha-4: “Crystal structure of trout hemoglobin at 1.35 ångström resolution”. X-ray diffraction, 2 ligands (HEM, ACE), 11 pockets (best druggability 0.85). MolNFT v1 #59131 on GenesisL1: 3D structure, binding…
- PDB
- 3BOM
- Type
- protein
- Length
- 578 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-4; Hemoglobin subunit beta-4
- UniProt
- P14527, P02141
- Ligands
- HEM, ACE
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha-4 | protein | 142 | 75% helix, 0% strand | P14527 |
| B, D | Hemoglobin subunit beta-4 | protein | 147 | 78% helix, 0% strand | P02141 |
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
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.85 | 0.87 | 68 | ACE |
| 2 | 244 | 0.73 | 0.87 | 33 | HEM |
| 3 | 209 | 0.71 | 0.87 | 25 | HEM |
| 4 | 246 | 0.71 | 0.85 | 29 | HEM |
| 5 | 216 | 0.70 | 0.86 | 24 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 875 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 875 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 672 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 668 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 449 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3BOM · Crystal structure of trout hemoglobin at 1.35 Angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P14527 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-4 (P14527) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P02141 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-4 (P02141) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P14527
- Every structure of UniProt P02141
- Elsewhere: RCSB PDB 3BOM · PDBe 3BOM · UniProt P14527 · UniProt P02141
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