MolNFT v1 · #112468 · protein
Crystal structure of circularly permuted human asparaginase-like protein 1
4ZM9 · Isoaspartyl PEPTIDASE/L-asparaginase: “Crystal structure of circularly permuted human asparaginase-like protein 1”. X-ray diffraction, 2 ligands (GLY, NA), 7 pockets (best druggability 0.60). MolNFT v1 #112468 on GenesisL1: 3D…
- PDB
- 4ZM9
- Type
- protein
- Length
- 1,184 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoaspartyl PEPTIDASE/L-asparaginase
- EC
- 3.4.19.5, 3.5.1.1
- UniProt
- Q7L266
- Ligands
- GLY, NA
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isoaspartyl PEPTIDASE/L-asparaginase (EC 3.4.19.5, 3.5.1.1) | protein | 296 | 35% helix, 26% strand | Q7L266 |
Ligands and binding sites
- GLY · Glycine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 10 copies · chains A, B, C, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, C
- FLC · Citrate anion · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.60 | 0.80 | 34 | FLC |
| 2 | 233 | 0.59 | 0.80 | 32 | FLC |
| 3 | 272 | 0.58 | 0.78 | 34 | DTT |
| 4 | 237 | 0.56 | 0.78 | 32 | DTT |
| 5 | 132 | 0.39 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1892 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1890 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 154 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ZM9 · Crystal structure of circularly permuted human asparaginase-like protein 1 · the same entry in another collection · chain C against C, TM-score 1.00
- Q7L266 · AlphaFold monomer V2.0 prediction for isoaspartyl PEPTIDASE/L-asparaginase (Q7L266) · a predicted model of the same protein · chain C 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 Q7L266
- Elsewhere: RCSB PDB 4ZM9 · PDBe 4ZM9 · UniProt Q7L266
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