MolNFT v1 · #15851 · protein
Structural insights into the processivity of endopolygalacturonase I from aspergillus niger
1NHC: “Structural insights into the processivity of endopolygalacturonase I from aspergillus niger”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 9 pockets (best druggability 0.77). MolNFT v1 #15851 on GenesisL1: 3D structure, binding…
- PDB
- 1NHC
- Type
- protein
- Length
- 2,016 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polygalacturonase I
- EC
- 3.2.1.15
- UniProt
- P26213
- Ligands
- MAN, NAG, BMA, SO4
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Polygalacturonase I (EC 3.2.1.15) | protein | 336 | 5% helix, 52% strand | P26213 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains E, D, A, B, C, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, E, D, C, F
- BMA · beta-D-mannopyranose · sugar · chains D, E
- SO4 · Sulfate ion · ion · 16 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 5 copies · chains A, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.77 | 0.83 | 95 | SO4 |
| 2 | 333 | 0.60 | 0.78 | 37 | empty |
| 3 | 239 | 0.48 | 0.74 | 38 | SO4 |
| 4 | 243 | 0.47 | 0.74 | 35 | SO4 |
| 5 | 210 | 0.47 | 0.75 | 31 | SO4 |
Interfaces
7 interfaces between chains.
- D–E · 737 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 306 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 268 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 242 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 207 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 17 glycan (disulfide, O-glycosylation, N-glycosylation).
Compared structures
- 1NHC · Structural insights into the processivity of endopolygalacturonase I from Aspergillus… · the same entry in another collection · chain E against E, TM-score 1.00
- P26213 · AlphaFold monomer V2.0 prediction for endopolygalacturonase I (P26213) · 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 P26213
- Elsewhere: RCSB PDB 1NHC · PDBe 1NHC · UniProt P26213
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