MolNFT v1 · #107532 · protein
Structure of the N terminal domain of the MERS cov nucleocapsid
4UD1 · N protein: “Structure of the N terminal domain of the MERS cov nucleocapsid”. X-ray diffraction, 1 ligand (NH4), 6 pockets (best druggability 0.72). MolNFT v1 #107532 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UD1
- Type
- protein
- Length
- 621 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N protein
- UniProt
- T2B9R0
- Ligands
- NH4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | N protein | protein | 133 | 2% helix, 32% strand | T2B9R0 |
| D | N protein | protein | 112 | 3% helix, 27% strand | T2B9R0 |
| E | N protein | protein | 110 | 3% helix, 20% strand | T2B9R0 |
Ligands and binding sites
- NH4 · Ammonium ion · ion · 4 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 3 copies · chains B, C, D
- IMD · Imidazole · additive · 2 copies · chains B, C
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 | 368 | 0.72 | 0.84 | 37 | empty |
| 2 | 376 | 0.72 | 0.83 | 38 | empty |
| 3 | 350 | 0.71 | 0.83 | 39 | empty |
| 4 | 58 | 0.52 | 0.87 | 23 | empty |
| 5 | 120 | 0.38 | 0.74 | 24 | empty |
Interfaces
7 interfaces between chains.
- A–B · 428 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 359 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 359 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 305 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 298 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4UD1 · Structure of the N Terminal domain of the MERS CoV nucleocapsid · 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 T2B9R0
- Elsewhere: RCSB PDB 4UD1 · PDBe 4UD1 · UniProt T2B9R0
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