Research workbench
Ebulin complexed with pteroic acid, trigonal crystal form
Analyse Ebulin complexed with pteroic acid, trigonal crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HWP
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ebulin
- EC
- 3.2.2.22
- UniProt
- Q9AVR2
- Ligands
- PT1, NAG, BGC, GAL, BMA
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ebulin (EC 3.2.2.22) | protein | 252 | 41% helix, 23% strand | Q9AVR2 |
| B | Ebulin (EC 3.2.2.22) | protein | 263 | 11% helix, 35% strand | Q9AVR2 |
Ligands and binding sites
- PT1 · Pteroic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- BGC · beta-D-glucopyranose · sugar · chains B
- GAL · beta-D-galactopyranose · sugar · chains B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.62 | 0.83 | 32 | empty |
| 2 | 57 | 0.60 | 0.92 | 20 | empty |
| 3 | 186 | 0.54 | 0.79 | 33 | PT1 |
| 4 | 115 | 0.47 | 0.79 | 21 | empty |
| 5 | 165 | 0.46 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1744 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1HWP · Ebulin complexed with pteroic acid, trigonal crystal form · the same entry in another collection · 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 Q9AVR2
- Elsewhere: RCSB PDB 1HWP · PDBe 1HWP · UniProt Q9AVR2
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