MolNFT v1 · #154745 · protein
Structure of the N-terminal domain of middle east respiratory syndrome coronavirus nucleocapsid protein complexed with benzyl 2- (hydroxymethyl)-1-indolinecarboxylate
6KL5 · Nucleoprotein: “Structure of the N-terminal domain of middle east respiratory syndrome coronavirus nucleocapsid protein…”. X-ray diffraction, 1 ligand (DJO), 4 pockets (best druggability 0.68). MolNFT v1 #154745 on GenesisL1: 3D…
- PDB
- 6KL5
- Type
- protein
- Length
- 445 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- A0A0D3MU65
- Ligands
- DJO
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 114 | 5% helix, 23% strand | A0A0D3MU65 |
| B | Nucleoprotein | protein | 123 | 2% helix, 26% strand | A0A0D3MU65 |
| C | Nucleoprotein | protein | 103 | 3% helix, 19% strand | A0A0D3MU65 |
| D | Nucleoprotein | protein | 105 | 6% helix, 20% strand | A0A0D3MU65 |
Ligands and binding sites
- DJO · (phenylmethyl) (2S)-2-(hydroxymethyl)-2,3-dihydroindole-1-carboxylate · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.68 | 0.80 | 56 | empty |
| 2 | 213 | 0.57 | 0.79 | 29 | DJO |
| 3 | 59 | 0.40 | 0.81 | 19 | empty |
| 4 | 68 | 0.28 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–D · 561 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 310 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 273 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6KL5 · Structure of The N-terminal domain of Middle East respiratory syndrome coronavirus… · 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 A0A0D3MU65
- Elsewhere: RCSB PDB 6KL5 · PDBe 6KL5 · UniProt A0A0D3MU65
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