MolNFT v1 · #11158 · protein
Chimeric HUMAN/MOUSE carbonmonoxy hemoglobin (human ZETA2 / mouse BETA2)
1JEB · Hemoglobin zeta chain: “Chimeric HUMAN/MOUSE carbonmonoxy hemoglobin (human ZETA2 / mouse BETA2)”. X-ray diffraction, 3 ligands (HEM, ACE, CMO), 5 pockets (best druggability 0.85). MolNFT v1 #11158 on GenesisL1: 3D structure…
- PDB
- 1JEB
- Type
- protein
- Length
- 571 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin zeta chain; Hemoglobin beta-single chain
- UniProt
- P02008, P02088
- Ligands
- HEM, ACE, CMO
- Pockets
- 5 · 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 zeta chain | protein | 141 | 76% helix, 0% strand | P02008 |
| B | Hemoglobin beta-single chain | protein | 143 | 79% helix, 0% strand | P02088 |
| D | Hemoglobin beta-single chain | protein | 146 | 78% helix, 0% strand | P02088 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.85 | 0.86 | 102 | empty |
| 2 | 271 | 0.77 | 0.89 | 38 | HEM, CMO |
| 3 | 270 | 0.76 | 0.88 | 29 | HEM, CMO |
| 4 | 253 | 0.73 | 0.86 | 26 | HEM, CMO |
| 5 | 217 | 0.72 | 0.87 | 25 | HEM, CMO |
Interfaces
6 interfaces between chains.
- A–B · 915 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 875 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 523 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 493 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 154 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1JEB · Chimeric Human/Mouse Carbonmonoxy Hemoglobin (Human Zeta2 / Mouse Beta2) · the same entry in another collection · chain A against A, TM-score 1.00
- P02008 · AlphaFold monomer V2.0 prediction for hemoglobin subunit zeta (P02008) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P02088 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-1 (P02088) · 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 P02008
- Every structure of UniProt P02088
- Elsewhere: RCSB PDB 1JEB · PDBe 1JEB · UniProt P02008 · UniProt P02088
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