Research workbench
LDTMT2 with covalent adduct derived from N-thio-beta-lactam 1A
Analyse LDTMT2 with covalent adduct derived from N-thio-beta-lactam 1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A1C
- Type
- protein
- Length
- 515 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
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 256 | 11% helix, 42% strand | I6Y9J2 |
| B | L,D-transpeptidase 2 (EC 2.3.2.-) | protein | 259 | 12% helix, 40% strand | I6Y9J2 |
Ligands and binding sites
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.82 | 0.83 | 105 | DMS |
| 2 | 109 | 0.39 | 0.75 | 20 | empty |
| 3 | 86 | 0.34 | 0.75 | 17 | empty |
| 4 | 61 | 0.29 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1027 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
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 7A1C · PDBe 7A1C · UniProt I6Y9J2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.