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Crystal structure of plii-ah, periplasmic lysozyme inhibitor of I-type lysozyme from aeromonas hydrophyla
Analyse Crystal structure of plii-ah, periplasmic lysozyme inhibitor of I-type lysozyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OD9
- Type
- protein
- Length
- 362 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative exported protein
- UniProt
- A0KHJ5
- Ligands
- NA, K
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative exported protein | protein | 122 | 5% helix, 52% strand | A0KHJ5 |
| B | Putative exported protein | protein | 120 | 5% helix, 53% strand | A0KHJ5 |
| C | Putative exported protein | protein | 120 | 4% helix, 53% strand | A0KHJ5 |
Ligands and binding sites
- NA · Sodium ion · metal · 10 copies · chains A, B, C
- K · Potassium ion · metal · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.55 | 0.83 | 24 | empty |
| 2 | 203 | 0.52 | 0.77 | 35 | empty |
Interfaces
2 interfaces between chains.
- A–B · 870 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 346 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3OD9 · Crystal structure of PliI-Ah, periplasmic lysozyme inhibitor of I-type lysozyme from… · 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 A0KHJ5
- Elsewhere: RCSB PDB 3OD9 · PDBe 3OD9 · UniProt A0KHJ5
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