Research workbench
Crystal structure of neisseria meningitidis vaccine antigen nada variant 3
Analyse Crystal structure of neisseria meningitidis vaccine antigen nada variant 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EUN
- Type
- protein
- Length
- 437 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adhesin
- UniProt
- A0ELI3
- Ligands
- P4G, PO4, CL
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adhesin | protein | 147 | 77% helix, 7% strand | A0ELI3 |
| B, C | Adhesin | protein | 145 | 77% helix, 7% strand | A0ELI3 |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 2 copies · chains A, C, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, B
- CL · Chloride ion · ion · chains A, B, C
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, C, A
- CIT · Citric acid · additive · chains A, B
- 2PE · Nonaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.72 | 0.96 | 17 | empty |
| 2 | 212 | 0.48 | 0.74 | 34 | EDO |
| 3 | 68 | 0.40 | 0.80 | 17 | EDO |
| 4 | 58 | 0.38 | 0.80 | 16 | empty |
| 5 | 140 | 0.38 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1914 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 1906 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1897 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6EUN · Crystal structure of Neisseria meningitidis vaccine antigen NadA variant 3 · 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 A0ELI3
- Elsewhere: RCSB PDB 6EUN · PDBe 6EUN · UniProt A0ELI3
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