Research workbench
Crystal structure of acetate-bound HELL'S gate globin I
Analyse Crystal structure of acetate-bound HELL'S gate globin I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S1J
- Type
- protein
- Length
- 393 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin-like flavoprotein
- UniProt
- B3DUZ7
- Ligands
- HEM, SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hemoglobin-like flavoprotein | protein | 131 | 83% helix, 0% strand | B3DUZ7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains B, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
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 | 324 | 0.75 | 0.86 | 41 | HEM, ACT |
| 2 | 294 | 0.75 | 0.87 | 33 | HEM, ACT |
| 3 | 284 | 0.74 | 0.86 | 34 | HEM, ACT |
| 4 | 70 | 0.30 | 0.74 | 14 | empty |
| 5 | 62 | 0.28 | 0.74 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 793 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 575 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3S1J · Crystal structure of acetate-bound hell's gate globin I · 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 B3DUZ7
- Elsewhere: RCSB PDB 3S1J · PDBe 3S1J · UniProt B3DUZ7
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