Research workbench
Structural investigations of the substrate specificity of human O- glcnacase
Analyse Structural investigations of the substrate specificity of human O- glcnacase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VVT
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-glcnacase; ELK1 peptide
- EC
- 3.2.1.169, 3.2.1.-
- UniProt
- O60502
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein O-glcnacase (EC 3.2.1.169, 3.2.1.-) | protein | 419 | 49% helix, 10% strand | O60502 |
| B | ELK1 peptide | protein | 2 | 0% helix, 0% strand | — |
| C | Protein O-glcnacase (EC 3.2.1.169, 3.2.1.-) | protein | 423 | 50% helix, 10% strand | O60502 |
| D | ELK1 peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.81 | 0.83 | 81 | empty |
| 2 | 59 | 0.71 | 0.97 | 23 | NAG |
| 3 | 59 | 0.66 | 0.95 | 17 | empty |
| 4 | 231 | 0.60 | 0.80 | 39 | NAG |
| 5 | 192 | 0.47 | 0.75 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–C · 3625 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 282 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 167 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 135 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 98 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (O-glycosylation).
Compared structures
- 5VVT · Structural Investigations of the Substrate Specificity of Human O-GlcNAcase · the same entry in another collection · chain A against A, TM-score 1.00
- O60502 · AlphaFold monomer V2.0 prediction for protein O-glcnacase (O60502) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 O60502
- Elsewhere: RCSB PDB 5VVT · PDBe 5VVT · UniProt O60502
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