Research workbench
Crystal structure of phosphate-bound HELL'S gate globin IV
Analyse Crystal structure of phosphate-bound HELL'S gate globin IV in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NK1
- Type
- protein
- Length
- 321 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin-like protein
- UniProt
- B3DVC3
- Ligands
- HEM, PO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin-like protein | protein | 160 | 58% helix, 4% strand | B3DVC3 |
| B | Hemoglobin-like protein | protein | 161 | 56% helix, 4% strand | B3DVC3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.77 | 0.87 | 30 | HEM, PO4 |
| 2 | 394 | 0.77 | 0.86 | 33 | HEM, PO4 |
| 3 | 57 | 0.71 | 0.98 | 18 | empty |
| 4 | 146 | 0.45 | 0.76 | 18 | empty |
| 5 | 125 | 0.44 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1331 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4NK1 · Crystal structure of phosphate-bound Hell's gate globin IV · 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 B3DVC3
- Elsewhere: RCSB PDB 4NK1 · PDBe 4NK1 · UniProt B3DVC3
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