Research workbench
Complex of the N-acetylmuramyl-L-alanine amidase amid from E.COLI with the product L-ala-D-gamma-glu-L-lys
Analyse Complex of the N-acetylmuramyl-L-alanine amidase amid from E.COLI with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D2Z
- Type
- protein
- Length
- 259 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylmuramoyl-L-alanine amidase amid; L-ala-D-gamma-glu-L-lys peptide
- EC
- 3.5.1.28
- UniProt
- P75820
- Ligands
- ZN, CL
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylmuramoyl-L-alanine amidase amid (EC 3.5.1.28) | protein | 256 | 34% helix, 17% strand | P75820 |
| B | L-ala-D-gamma-glu-L-lys peptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.31 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 317 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 3D2Z · Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the product… · the same entry in another collection · chain A against A, TM-score 1.00
- P75820 · AlphaFold monomer V2.0 prediction for N-acetylmuramoyl-L-alanine amidase amid (P75820) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P75820
- Elsewhere: RCSB PDB 3D2Z · PDBe 3D2Z · UniProt P75820
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.