MolNFT v1 · #172401 · protein
Lpps with covalent adduct derived from 1C
7A1E · L,D-transpeptidase 2: “Lpps with covalent adduct derived from 1C”. X-ray diffraction, 1 ligand (SDQ), 4 pockets (best druggability 0.81). MolNFT v1 #172401 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7A1E
- 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
- SDQ
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 259 | 12% helix, 41% strand | I6Y9J2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.81 | 0.82 | 102 | ACT |
| 2 | 198 | 0.52 | 0.77 | 33 | SDQ |
| 3 | 137 | 0.44 | 0.76 | 28 | empty |
| 4 | 76 | 0.34 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1123 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 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 7A1E · PDBe 7A1E · UniProt I6Y9J2
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