Research workbench
The crystal structure of LY7917 with the hydrolyzing product of mdp
Analyse The crystal structure of LY7917 with the hydrolyzing product of mdp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D76
- Type
- protein
- Length
- 463 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative phage lysin
- UniProt
- M1PKZ3
- Ligands
- 58B, CL
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative phage lysin | protein | 231 | 17% helix, 42% strand | M1PKZ3 |
| B | Putative phage lysin | protein | 232 | 14% helix, 42% strand | M1PKZ3 |
Ligands and binding sites
- 58B · L-alanyl-D-alpha-glutamine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.62 | 0.78 | 51 | 58B |
| 2 | 120 | 0.40 | 0.75 | 22 | empty |
| 3 | 54 | 0.39 | 0.81 | 15 | 58B |
| 4 | 81 | 0.35 | 0.75 | 20 | empty |
| 5 | 73 | 0.34 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 545 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5D76 · The crystal structure of Ly7917 with the hydrolyzing product of MDP · 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 M1PKZ3
- Elsewhere: RCSB PDB 5D76 · PDBe 5D76 · UniProt M1PKZ3
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