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The crystal structure of SARS NSP10 without zinc ion as additive
Analyse The crystal structure of SARS NSP10 without zinc ion as additive in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GA6
- Type
- protein
- Length
- 2,835 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ORF1A polyprotein
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G, H, I, J, K, L, M, O, P, Q, S, T, U, V, W, X | ORF1A polyprotein | protein | 118 | 29% helix, 15% strand | — |
| B, N | ORF1A polyprotein | protein | 119 | 33% helix, 15% strand | — |
| F | ORF1A polyprotein | protein | 120 | 30% helix, 16% strand | — |
| R | ORF1A polyprotein | protein | 117 | 32% helix, 15% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 48 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.83 | 0.84 | 94 | empty |
| 2 | 988 | 0.83 | 0.84 | 101 | empty |
| 3 | 1138 | 0.83 | 0.84 | 118 | empty |
| 4 | 1002 | 0.83 | 0.84 | 101 | empty |
| 5 | 1193 | 0.83 | 0.84 | 116 | empty |
Interfaces
64 interfaces between chains.
- I–M · 493 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 420 Ų buried · 3 hydrogen bonds · protein-protein
- N–T · 384 Ų buried · 3 hydrogen bonds · protein-protein
- B–H · 382 Ų buried · 4 hydrogen bonds · protein-protein
- F–L · 368 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 79 disulfide (disulfide).
Compared structures
- 2GA6 · The crystal structure of SARS nsp10 without zinc ion as additive · 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
- Elsewhere: RCSB PDB 2GA6 · PDBe 2GA6
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