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The structure of L-pgs from bacillus licheniformis
Analyse The structure of L-pgs from bacillus licheniformis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4V36
- Type
- protein
- Length
- 639 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysyl-tRNA-dependent L-ysyl-phosphatidylgycerol synthase
- EC
- 2.3.2.3
- UniProt
- E5W5M1
- Ligands
- LYN
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysyl-tRNA-dependent L-ysyl-phosphatidylgycerol synthase (EC 2.3.2.3) | protein | 325 | 36% helix, 25% strand | E5W5M1 |
| B | Lysyl-tRNA-dependent L-ysyl-phosphatidylgycerol synthase (EC 2.3.2.3) | protein | 314 | 38% helix, 28% strand | E5W5M1 |
Ligands and binding sites
- LYN · 2,6-diamino-hexanoic acid amide · ligand · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.83 | 0.84 | 98 | empty |
| 2 | 309 | 0.75 | 0.87 | 38 | LYN |
| 3 | 131 | 0.49 | 0.79 | 25 | empty |
| 4 | 67 | 0.47 | 0.83 | 19 | empty |
| 5 | 135 | 0.42 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 476 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4V36 · The structure of L-PGS from Bacillus licheniformis · 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 E5W5M1
- Elsewhere: RCSB PDB 4V36 · PDBe 4V36 · UniProt E5W5M1
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