Research workbench
SARS-cov NSP10/NSP14 dynamic complex
Analyse SARS-cov NSP10/NSP14 dynamic complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NFY
- Type
- protein
- Length
- 2,585 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein 1AB
- UniProt
- Q1T6X8
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyprotein 1AB | protein | 512 | 24% helix, 23% strand | Q1T6X8 |
| B, C, D | Polyprotein 1AB | protein | 514 | 24% helix, 23% strand | Q1T6X8 |
| M | Polyprotein 1AB | protein | 132 | 27% helix, 14% strand | Q1T6X8 |
| N, O, P | Polyprotein 1AB | protein | 133 | 29% helix, 15% strand | Q1T6X8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 20 copies · chains A, B, C, D, M, N, O, P
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.77 | 0.83 | 44 | empty |
| 2 | 610 | 0.75 | 0.82 | 58 | empty |
| 3 | 837 | 0.75 | 0.79 | 81 | empty |
| 4 | 687 | 0.71 | 0.78 | 41 | empty |
| 5 | 766 | 0.70 | 0.76 | 50 | empty |
Interfaces
7 interfaces between chains.
- C–P · 2348 Ų buried · 30 hydrogen bonds · protein-protein
- B–N · 2347 Ų buried · 27 hydrogen bonds · protein-protein
- D–O · 2321 Ų buried · 25 hydrogen bonds · protein-protein
- A–M · 2303 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5NFY · SARS-CoV nsp10/nsp14 dynamic complex · 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 Q1T6X8
- Elsewhere: RCSB PDB 5NFY · PDBe 5NFY · UniProt Q1T6X8
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