MolNFT v1 · #141776 · protein
Crystal structure of hexacoordinated heme protein from anhydrobiotic tardigrade at pH 4
5ZIQ · Globin protein: “Crystal structure of hexacoordinated heme protein from anhydrobiotic tardigrade at pH 4”. X-ray diffraction, 2 ligands (HEM, SO4), 4 pockets (best druggability 0.82). MolNFT v1 #141776 on GenesisL1: 3D structure…
- PDB
- 5ZIQ
- Type
- protein
- Length
- 617 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Globin protein
- UniProt
- A0A1D1V896
- Ligands
- HEM, SO4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Globin protein | protein | 155 | 80% helix, 0% strand | A0A1D1V896 |
| D | Globin protein | protein | 152 | 80% helix, 0% strand | A0A1D1V896 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.82 | 0.88 | 72 | HEM |
| 2 | 744 | 0.80 | 0.83 | 77 | HEM |
| 3 | 485 | 0.75 | 0.83 | 47 | empty |
| 4 | 184 | 0.70 | 0.87 | 23 | HEM |
Interfaces
5 interfaces between chains.
- A–B · 851 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 824 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 340 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 282 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 275 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5ZIQ · Crystal structure of hexacoordinated heme protein from anhydrobiotic tardigrade at pH 4 · the same entry in another collection · chain A against A, 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 A0A1D1V896
- Elsewhere: RCSB PDB 5ZIQ · PDBe 5ZIQ · UniProt A0A1D1V896
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