Research workbench
Crystal structure of allantoate-amidohydrolase from E.COLI K12 in complex with substrate allantoate
Analyse Crystal structure of allantoate-amidohydrolase from E.COLI K12 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z2L
- Type
- protein
- Length
- 821 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allantoate amidohydrolase
- EC
- 3.5.3.-
- UniProt
- P77425
- Ligands
- 1AL, ZN, SO4
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Allantoate amidohydrolase (EC 3.5.3.-) | protein | 411 | 37% helix, 25% strand | P77425 |
| B | Allantoate amidohydrolase (EC 3.5.3.-) | protein | 410 | 38% helix, 25% strand | P77425 |
Ligands and binding sites
- 1AL · Allantoate ion · ligand · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.60 | 0.76 | 39 | ZN, SO4, 1AL |
| 2 | 358 | 0.60 | 0.77 | 38 | ZN, SO4 |
| 3 | 70 | 0.47 | 0.83 | 20 | empty |
| 4 | 67 | 0.43 | 0.81 | 20 | empty |
| 5 | 57 | 0.41 | 0.81 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 2265 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1Z2L · Crystal structure of Allantoate-amidohydrolase from E.coli K12 in complex with substrate… · the same entry in another collection · chain A against A, TM-score 1.00
- P77425 · AlphaFold monomer V2.0 prediction for allantoate amidohydrolase (P77425) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P77425
- Elsewhere: RCSB PDB 1Z2L · PDBe 1Z2L · UniProt P77425
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