MolNFT v1 · #18439 · protein
The crystal structure of rhamnogalacturonan acetylesterase in space group P3121
1PP4: “The crystal structure of rhamnogalacturonan acetylesterase in space group P3121”. X-ray diffraction, 1 ligand (NAG), 1 pocket (best druggability 0.72). MolNFT v1 #18439 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1PP4
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhamnogalacturonan acetylesterase
- EC
- 3.1.1.-
- UniProt
- Q00017
- Ligands
- NAG
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rhamnogalacturonan acetylesterase (EC 3.1.1.-) | protein | 233 | 39% helix, 16% strand | Q00017 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.72 | 0.77 | 84 | empty |
Interfaces
1 interface between chains.
- A–B · 634 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1PP4 · The crystal structure of rhamnogalacturonan acetylesterase in space group P3121 · the same entry in another collection · chain A against A, TM-score 1.00
- Q00017 · AlphaFold monomer V2.0 prediction for rhamnogalacturonan acetylesterase (Q00017) · a predicted model of the same protein · chain A 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 Q00017
- Elsewhere: RCSB PDB 1PP4 · PDBe 1PP4 · UniProt Q00017
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