Research workbench
Crystal structure of an asymmetric dimer of the N-terminal domain of euprosthenops australis major ampullate spidroin 1 (dragline silk)
Analyse Crystal structure of an asymmetric dimer of the N-terminal domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R9D
- Type
- protein
- Length
- 746 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major ampullate spidroin 1
- UniProt
- Q05H60
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major ampullate spidroin 1 | protein | 127 | 74% helix, 0% strand | Q05H60 |
| B | Major ampullate spidroin 1 | protein | 126 | 75% helix, 0% strand | Q05H60 |
| C, D, E | Major ampullate spidroin 1 | protein | 124 | 75% helix, 0% strand | Q05H60 |
| F | Major ampullate spidroin 1 | protein | 121 | 75% helix, 0% strand | Q05H60 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.65 | 0.76 | 66 | empty |
| 2 | 198 | 0.45 | 0.74 | 29 | empty |
| 3 | 100 | 0.42 | 0.77 | 14 | empty |
| 4 | 67 | 0.39 | 0.79 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1298 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1221 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1195 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 508 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 495 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6R9D · Crystal structure of an asymmetric dimer of the N-terminal domain of Euprosthenops… · 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 Q05H60
- Elsewhere: RCSB PDB 6R9D · PDBe 6R9D · UniProt Q05H60
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