Research workbench
Lpps with covalent adduct derived from 1B
Analyse Lpps with covalent adduct derived from 1B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A0Z
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L,D-transpeptidase 2
- EC
- 2.3.2.-
- UniProt
- I6Y9J2
- Ligands
- BT6, TAM
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 259 | 12% helix, 40% strand | I6Y9J2 |
Ligands and binding sites
- BT6 · benzenethiol · ligand · 2 copies · chains A, B
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.78 | 0.82 | 84 | empty |
| 2 | 178 | 0.54 | 0.79 | 31 | BT6 |
| 3 | 194 | 0.53 | 0.78 | 32 | BT6, TAM |
| 4 | 117 | 0.47 | 0.80 | 24 | empty |
| 5 | 82 | 0.37 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1193 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 I6Y9J2
- Elsewhere: RCSB PDB 7A0Z · PDBe 7A0Z · UniProt I6Y9J2
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