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Structural insight into host cell surface retention of a 1.5-mda bacterial ice-binding adhesin
Analyse Structural insight into host cell surface retention of a 1.5-mda bacterial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IRB
- Type
- protein
- Length
- 627 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rtx-adhesin
- UniProt
- A1YIY2
- Ligands
- CA, MG
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rtx-adhesin | protein | 313 | 10% helix, 54% strand | A1YIY2 |
| B | Rtx-adhesin | protein | 314 | 10% helix, 55% strand | A1YIY2 |
Ligands and binding sites
- CA · Calcium ion · metal · 17 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.54 | 0.82 | 27 | empty |
| 2 | 50 | 0.28 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 770 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5IRB · Structural insight into host cell surface retention of a 1.5-MDa bacterial ice-binding… · 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 A1YIY2
- Elsewhere: RCSB PDB 5IRB · PDBe 5IRB · UniProt A1YIY2
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