MolNFT v1 · #115077 · protein
Crystal structure of the SARS coronavirus NSP14-NSP10 complex with functional ligand SAM
5C8T · Non-structural protein 10: “Crystal structure of the SARS coronavirus NSP14-NSP10 complex with functional ligand SAM”. X-ray diffraction, 3 ligands (SAM, ZN, MG), 16 pockets (best druggability 0.82). MolNFT v1 #115077 on GenesisL1…
- PDB
- 5C8T
- Type
- protein
- Length
- 1,294 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 10; Guanine-N7 methyltransferase
- EC
- 2.1.1.-, 3.1.13.-
- UniProt
- P0C6X7
- Ligands
- SAM, ZN, MG
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Non-structural protein 10 | protein | 133 | 31% helix, 14% strand | P0C6X7 |
| B, D | Guanine-N7 methyltransferase (EC 2.1.1.-, 3.1.13.-) | protein | 514 | 25% helix, 21% strand | P0C6X7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains B, D
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.82 | 0.83 | 66 | SAM |
| 2 | 666 | 0.74 | 0.80 | 62 | SAM |
| 3 | 412 | 0.68 | 0.80 | 43 | empty |
| 4 | 50 | 0.63 | 0.94 | 16 | empty |
| 5 | 138 | 0.61 | 0.84 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2265 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2240 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 808 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5C8T · Crystal structure of the SARS coronavirus nsp14-nsp10 complex with functional ligand SAM · 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 P0C6X7
- Elsewhere: RCSB PDB 5C8T · PDBe 5C8T · UniProt P0C6X7
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