Research workbench
Crystal structure of Hyp-1, a St John's wort PR-10 protein, in complex with 8-anilino-1-naphthalene sulfonate (ANS)
Analyse Crystal structure of Hyp-1, a St John's wort PR-10 protein, in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N3E
- Type
- protein
- Length
- 4,452 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.43
- Source
- Hypericum perforatum
- Molecule
- Phenolic oxidative coupling protein
- UniProt
- Q8H1L1
- Ligands
- 2AN, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.43 · 1 distinct chain · 30% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b | Phenolic oxidative coupling protein | protein | 159 | 30% helix, 39% strand | Q8H1L1 |
Ligands and binding sites
- 2AN · 8-anilino-1-naphthalene sulfonate · ligand · 89 copies · chains A, B, Z, b, C, D, E, F, G, H, I, J, K, L, R, P, M, N, O, Q, S, U, W, V, X, Y, a
- SO4 · Sulfate ion · ion · 3 copies · chains V, X, b
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains C, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.83 | 0.90 | 51 | 2AN |
| 2 | 429 | 0.83 | 0.90 | 47 | 2AN |
| 3 | 445 | 0.83 | 0.89 | 50 | 2AN |
| 4 | 411 | 0.82 | 0.90 | 52 | 2AN |
| 5 | 485 | 0.82 | 0.89 | 64 | 2AN |
Interfaces
47 interfaces between chains.
- I–S · 508 Ų buried · 2 hydrogen bonds · protein-protein
- U–V · 496 Ų buried · 6 hydrogen bonds · protein-protein
- F–V · 495 Ų buried · 1 hydrogen bond · protein-protein
- B–Z · 479 Ų buried · 2 hydrogen bonds · protein-protein
- J–R · 476 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4N3E · Crystal structure of hyp-1, a st JOHN'S wort pr-10 protein, in complex with… · the same entry in another collection · chain B against B, 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 Q8H1L1
- Elsewhere: RCSB PDB 4N3E · PDBe 4N3E · UniProt Q8H1L1
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