Research workbench
Crystal structure of aeromonas hydrophila plii in complex with meretrix lusoria lysozyme
Analyse Crystal structure of aeromonas hydrophila plii in complex with meretrix lusoria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PJ2
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative exported protein; Lysozyme
- EC
- 3.2.1.17
- UniProt
- A0KHJ5, P86383
- Ligands
- MG
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative exported protein | protein | 121 | 5% helix, 52% strand | A0KHJ5 |
| B | Putative exported protein | protein | 123 | 5% helix, 50% strand | A0KHJ5 |
| C, D | Lysozyme (EC 3.2.1.17) | protein | 122 | 52% helix, 5% strand | P86383 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.56 | 0.82 | 29 | empty |
| 2 | 127 | 0.52 | 0.81 | 26 | GOL |
| 3 | 83 | 0.45 | 0.81 | 19 | GOL |
| 4 | 76 | 0.31 | 0.74 | 20 | empty |
| 5 | 59 | 0.28 | 0.74 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 857 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 827 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 770 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 269 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 246 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 4PJ2 · Crystal structure of Aeromonas hydrophila PliI in complex with Meretrix lusoria lysozyme · the same entry in another collection · chain A against A, TM-score 1.00
- P86383 · AlphaFold monomer V2.0 prediction for lysozyme (P86383) · a predicted model of the same protein · chain C against A, TM-score 0.99
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
- Every structure of UniProt P86383
- Elsewhere: RCSB PDB 4PJ2 · PDBe 4PJ2 · UniProt A0KHJ5 · UniProt P86383
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