MolNFT v1 · #39730 · protein
Crystal structure of vaccinia virus N1L protein
2I39 · Protein N1: “Crystal structure of vaccinia virus N1L protein”. X-ray diffraction, 9 pockets (best druggability 0.73). MolNFT v1 #39730 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2I39
- Type
- protein
- Length
- 710 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein N1
- UniProt
- P21054
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein N1 | protein | 117 | 74% helix, 0% strand | P21054 |
| B, D | Protein N1 | protein | 119 | 76% helix, 0% strand | P21054 |
| C | Protein N1 | protein | 119 | 76% helix, 0% strand | P21054 |
| E, F | Protein N1 | protein | 118 | 75% helix, 0% strand | P21054 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, C, D, E, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.73 | 0.80 | 90 | MPD |
| 2 | 544 | 0.71 | 0.80 | 56 | empty |
| 3 | 532 | 0.66 | 0.77 | 46 | MPD |
| 4 | 162 | 0.54 | 0.80 | 28 | empty |
| 5 | 147 | 0.49 | 0.79 | 29 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1177 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1173 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1135 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 713 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 324 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2I39 · Crystal structure of Vaccinia virus N1L protein · the same entry in another collection · chain C against C, 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 P21054
- Elsewhere: RCSB PDB 2I39 · PDBe 2I39 · UniProt P21054
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