Research workbench
Crystal structure analysis of hellethionin D
Analyse Crystal structure analysis of hellethionin D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SZS
- Type
- protein
- Length
- 318 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hellethionin-D
- UniProt
- P60057
- Ligands
- NA, CL
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hellethionin-D | protein | 42 | 45% helix, 17% strand | P60057 |
| B, C, D, E, F, G | Hellethionin-D | protein | 46 | 43% helix, 13% strand | P60057 |
Ligands and binding sites
- NA · Sodium ion · metal · 19 copies · chains A, E, B, D, G, F
- CL · Chloride ion · ion · 33 copies · chains A, E, G, F, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.56 | 0.84 | 24 | NA |
| 2 | 247 | 0.53 | 0.76 | 38 | CL |
| 3 | 165 | 0.47 | 0.76 | 24 | empty |
| 4 | 99 | 0.34 | 0.73 | 17 | CL |
| 5 | 58 | 0.30 | 0.75 | 12 | empty |
Interfaces
14 interfaces between chains.
- B–C · 435 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 372 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 334 Ų buried · 0 hydrogen bonds · protein-protein
- E–G · 292 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 287 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
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 P60057
- Elsewhere: RCSB PDB 3SZS · PDBe 3SZS · UniProt P60057
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