Research workbench
The crystal structure of the putative N-acetylmuramoyl-L- alanine amidase from neisseria meningitidis
Analyse The crystal structure of the putative N-acetylmuramoyl-L- alanine amidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CZX
- Type
- protein
- Length
- 726 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative N-acetylmuramoyl-L-alanine amidase
- UniProt
- Q9JZE9
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative N-acetylmuramoyl-L-alanine amidase | protein | 182 | 45% helix, 18% strand | Q9JZE9 |
| D | Putative N-acetylmuramoyl-L-alanine amidase | protein | 180 | 45% helix, 19% strand | Q9JZE9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.74 | 0.98 | 22 | empty |
| 2 | 76 | 0.73 | 0.97 | 26 | empty |
| 3 | 224 | 0.57 | 0.79 | 39 | empty |
| 4 | 199 | 0.54 | 0.79 | 35 | empty |
| 5 | 255 | 0.49 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 735 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 727 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 57 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3CZX · The crystal structure of the putative N-acetylmuramoyl-L-alanine amidase from Neisseria… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9JZE9
- Elsewhere: RCSB PDB 3CZX · PDBe 3CZX · UniProt Q9JZE9
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