Research workbench
Crystal structure of murein-tripeptide amidase mpaa from escherichia COLI O157
Analyse Crystal structure of murein-tripeptide amidase mpaa from escherichia COLI O157 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HXD
- Type
- protein
- Length
- 471 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein mpaa
- UniProt
- P0ACV7
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein mpaa | protein | 237 | 30% helix, 19% strand | P0ACV7 |
| B | Protein mpaa | protein | 234 | 30% helix, 19% strand | P0ACV7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.74 | 0.86 | 47 | ZN, CAC |
| 2 | 283 | 0.67 | 0.83 | 34 | ZN, CAC |
| 3 | 71 | 0.36 | 0.77 | 18 | empty |
| 4 | 63 | 0.33 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2079 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5HXD · Crystal structure of murein-tripeptide amidase MpaA from Escherichia coli O157 · the same entry in another collection · chain A against A, TM-score 1.00
- P0ACV7 · AlphaFold monomer V2.0 prediction for murein peptide amidase a (P0ACV7) · 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 P0ACV7
- Elsewhere: RCSB PDB 5HXD · PDBe 5HXD · UniProt P0ACV7
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