Research workbench
Crystal structure of acostatin from agkistrodon contortrix contortrix
Analyse Crystal structure of acostatin from agkistrodon contortrix contortrix in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C05
- Type
- protein
- Length
- 232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disintegrin acostatin alpha; Disintegrin acostatin-beta
- UniProt
- Q805F7, Q805F6
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Disintegrin acostatin alpha | protein | 59 | 0% helix, 22% strand | Q805F7 |
| B | Disintegrin acostatin-beta | protein | 59 | 0% helix, 22% strand | Q805F6 |
| C | Disintegrin acostatin alpha | protein | 58 | 0% helix, 22% strand | Q805F7 |
| D | Disintegrin acostatin-beta | protein | 56 | 0% helix, 23% strand | Q805F6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.57 | 0.82 | 27 | empty |
| 2 | 112 | 0.46 | 0.79 | 28 | empty |
| 3 | 99 | 0.36 | 0.74 | 27 | empty |
Interfaces
5 interfaces between chains.
- C–D · 447 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 393 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 357 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 277 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 174 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3C05 · Crystal structure of Acostatin from Agkistrodon Contortrix Contortrix · the same entry in another collection · chain D against D, TM-score 1.00
- Q805F6 · AlphaFold monomer V2.0 prediction for zinc METALLOPROTEINASE/DISINTEGRIN (Q805F6) · a predicted model of the same protein · chain D against A, TM-score 0.93
- Q805F7 · AlphaFold monomer V2.0 prediction for disintegrin acostatin-alpha (Q805F7) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 Q805F7
- Every structure of UniProt Q805F6
- Elsewhere: RCSB PDB 3C05 · PDBe 3C05 · UniProt Q805F7 · UniProt Q805F6
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