Research workbench
Crystal structure of ancylostoma ceylanicum excretory-secretory protein 2
Analyse Crystal structure of ancylostoma ceylanicum excretory-secretory protein 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NSW
- Type
- protein
- Length
- 730 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Excretory-secretory protein 2
- UniProt
- Q6R7N7
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Excretory-secretory protein 2 | protein | 106 | 17% helix, 39% strand | Q6R7N7 |
| G | Excretory-secretory protein 2 | protein | 94 | 14% helix, 43% strand | Q6R7N7 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.62 | 0.75 | 50 | empty |
| 2 | 414 | 0.60 | 0.76 | 40 | EPE |
| 3 | 252 | 0.52 | 0.76 | 34 | empty |
| 4 | 220 | 0.50 | 0.76 | 29 | empty |
| 5 | 142 | 0.39 | 0.74 | 21 | empty |
Interfaces
8 interfaces between chains.
- B–F · 487 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 487 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 479 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 274 Ų buried · 2 hydrogen bonds · protein-protein
- B–G · 255 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 3NSW · Crystal Structure of Ancylostoma ceylanicum Excretory-Secretory Protein 2 · 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 Q6R7N7
- Elsewhere: RCSB PDB 3NSW · PDBe 3NSW · UniProt Q6R7N7
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