MolNFT v1 · #58955 · protein
Met-perch hemoglobin at pH 8.0
3BJ3 · Hemoglobin alpha: “Met-perch hemoglobin at pH 8.0”. X-ray diffraction, 2 ligands (HEM, ACE), 10 pockets (best druggability 0.79). MolNFT v1 #58955 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BJ3
- Type
- protein
- Length
- 576 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha; Hemoglobin beta
- Ligands
- HEM, ACE
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin alpha | protein | 142 | 77% helix, 0% strand | — |
| B, D | Hemoglobin beta | protein | 146 | 76% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.79 | 0.89 | 47 | ACE |
| 2 | 285 | 0.76 | 0.88 | 43 | empty |
| 3 | 229 | 0.74 | 0.88 | 29 | HEM |
| 4 | 246 | 0.73 | 0.87 | 29 | HEM |
| 5 | 219 | 0.73 | 0.87 | 29 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 902 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 875 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 618 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 559 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 512 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3BJ3 · met-Perch hemoglobin at pH 8.0 · the same entry in another collection · chain B against B, 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 3BJ3 · PDBe 3BJ3
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