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X-ray crystal structure of a hyperactive, CA2+-dependent, beta-helical antifreeze protein from an antarctic bacterium
Analyse X-ray crystal structure of a hyperactive, CA2+-dependent, beta-helical… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P4G
- Type
- protein
- Length
- 1,227 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antifreeze protein
- UniProt
- A1YIY3
- Ligands
- CA, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antifreeze protein | protein | 301 | 4% helix, 35% strand | A1YIY3 |
| B | Antifreeze protein | protein | 313 | 4% helix, 34% strand | A1YIY3 |
| C | Antifreeze protein | protein | 301 | 4% helix, 35% strand | A1YIY3 |
| D | Antifreeze protein | protein | 312 | 4% helix, 34% strand | A1YIY3 |
Ligands and binding sites
- CA · Calcium ion · metal · 52 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, C, B
- ACT · Acetate ion · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.80 | 0.83 | 85 | MG |
| 2 | 1053 | 0.76 | 0.79 | 92 | empty |
| 3 | 202 | 0.57 | 0.80 | 41 | ACT |
| 4 | 399 | 0.55 | 0.74 | 64 | empty |
| 5 | 92 | 0.34 | 0.74 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1535 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 893 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 630 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 144 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 141 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3P4G · X-ray crystal structure of a hyperactive, Ca2+-dependent, beta-helical antifreeze protein… · 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 A1YIY3
- Elsewhere: RCSB PDB 3P4G · PDBe 3P4G · UniProt A1YIY3
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