MolNFT v1 · #124422 · protein
Deer mouse recombinant hemoglobin from high altitude species
5KER · Alpha-globin: “Deer mouse recombinant hemoglobin from high altitude species”. X-ray diffraction, 1 ligand (HEM), 15 pockets (best druggability 0.85). MolNFT v1 #124422 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KER
- Type
- protein
- Length
- 1,144 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-globin; Beta globin
- UniProt
- A4ZQ87, B7SBL4
- Ligands
- HEM
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E, G, A | Alpha-globin | protein | 140 | 79% helix, 0% strand | A4ZQ87 |
| D, F, H, B | Beta globin | protein | 146 | 74% helix, 0% strand | B7SBL4 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains C, D, E, F, G, H, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.85 | 0.86 | 120 | empty |
| 2 | 858 | 0.84 | 0.86 | 113 | empty |
| 3 | 282 | 0.77 | 0.88 | 42 | HEM |
| 4 | 229 | 0.75 | 0.88 | 26 | HEM |
| 5 | 225 | 0.74 | 0.88 | 28 | HEM |
Interfaces
15 interfaces between chains.
- A–B · 899 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 873 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 854 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 835 Ų buried · 11 hydrogen bonds · protein-protein
- E–H · 510 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5KER · Deer mouse recombinant hemoglobin from high altitude species · the same entry in another collection · chain C against C, 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
- Every structure of UniProt A4ZQ87
- Every structure of UniProt B7SBL4
- Elsewhere: RCSB PDB 5KER · PDBe 5KER · UniProt A4ZQ87 · UniProt B7SBL4
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