MolNFT v1 · #40389 · protein
Crystal structure of the polygalacturonase from colletotrichum lupini and its implications for the interaction with polygalacturonase- inhibiting proteins
2IQ7 · Endopolygalacturonase: “Crystal structure of the polygalacturonase from colletotrichum lupini and its implications for the…”. X-ray diffraction, 2 ligands (NAG, MAN), 11 pockets (best druggability 0.78). MolNFT v1 #40389 on…
- PDB
- 2IQ7
- Type
- protein
- Length
- 2,372 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endopolygalacturonase
- EC
- 3.2.1.15
- UniProt
- A1E266
- Ligands
- NAG, MAN
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G | Endopolygalacturonase (EC 3.2.1.15) | protein | 339 | 6% helix, 52% strand | A1E266 |
| F | Endopolygalacturonase (EC 3.2.1.15) | protein | 338 | 6% helix, 52% strand | A1E266 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, E, B, C, D, F, G
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains E, A
- PG4 · Tetraethylene glycol · additive · 6 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, E, F
- ACY · Acetic acid · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.78 | 0.80 | 140 | PEG |
| 2 | 906 | 0.74 | 0.78 | 117 | empty |
| 3 | 792 | 0.70 | 0.77 | 96 | ACY |
| 4 | 451 | 0.58 | 0.74 | 56 | empty |
| 5 | 225 | 0.47 | 0.74 | 40 | empty |
Interfaces
10 interfaces between chains.
- A–C · 615 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 533 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 522 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 386 Ų buried · 4 hydrogen bonds · protein-protein
- A–G · 301 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 2IQ7 · Crystal structure of the polygalacturonase from Colletotrichum lupini and its… · the same entry in another collection · chain E against E, 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 A1E266
- Elsewhere: RCSB PDB 2IQ7 · PDBe 2IQ7 · UniProt A1E266
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