Research workbench
Lpps with covalent adduct derived from 1G
Analyse Lpps with covalent adduct derived from 1G in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A10
- Type
- protein
- Length
- 517 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
- QU5
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 259 | 11% helix, 41% strand | I6Y9J2 |
| B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 258 | 12% helix, 40% strand | I6Y9J2 |
Ligands and binding sites
- QU5 · 4-methoxycyclohexa-2,5-diene-1-thione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.79 | 0.84 | 86 | empty |
| 2 | 262 | 0.59 | 0.79 | 34 | QU5 |
| 3 | 129 | 0.48 | 0.79 | 24 | empty |
| 4 | 74 | 0.47 | 0.82 | 14 | QU5 |
| 5 | 122 | 0.39 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1137 Ų buried · 15 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 7A10 · PDBe 7A10 · UniProt I6Y9J2
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