MolNFT v1 · #38055 · protein
Crystal structure of glycosylasparaginase-substrate complex
2GL9 · Glycosylasparaginase alpha chain: “Crystal structure of glycosylasparaginase-substrate complex”. X-ray diffraction, 2 ligands (ASN, NAG), 7 pockets (best druggability 0.58). MolNFT v1 #38055 on GenesisL1: 3D structure, binding sites…
- PDB
- 2GL9
- Type
- protein
- Length
- 570 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosylasparaginase alpha chain; Glycosylasparaginase beta chain
- EC
- 3.5.1.26
- UniProt
- Q47898
- Ligands
- ASN, NAG
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosylasparaginase alpha chain (EC 3.5.1.26) | protein | 140 | 44% helix, 15% strand | Q47898 |
| B, D | Glycosylasparaginase beta chain (EC 3.5.1.26) | protein | 144 | 26% helix, 38% strand | Q47898 |
| C | Glycosylasparaginase alpha chain (EC 3.5.1.26) | protein | 142 | 43% helix, 15% strand | Q47898 |
Ligands and binding sites
- ASN · Asparagine · ligand · 2 copies · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, C, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.58 | 0.88 | 26 | empty |
| 2 | 130 | 0.45 | 0.77 | 23 | NAG, ASN |
| 3 | 131 | 0.43 | 0.76 | 23 | NAG, ASN |
| 4 | 57 | 0.42 | 0.82 | 16 | empty |
| 5 | 51 | 0.38 | 0.81 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2698 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2684 Ų buried · 53 hydrogen bonds · protein-protein
- A–D · 710 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 705 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 689 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2GL9 · Crystal Structure of Glycosylasparaginase-Substrate Complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q47898 · AlphaFold monomer V2.0 prediction for N(4)-(beta-N- acetylglucosaminyl)-L-asparaginase… · a predicted model of the same protein · chain D 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 Q47898
- Elsewhere: RCSB PDB 2GL9 · PDBe 2GL9 · UniProt Q47898
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