Research workbench
The crystal structure of SARS coronavirus orf-9B protein
Analyse The crystal structure of SARS coronavirus orf-9B protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CME
- Type
- protein
- Length
- 615 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein 5
- UniProt
- P59636
- Ligands
- D10
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein 5 | protein | 78 | 4% helix, 45% strand | P59636 |
| B | Hypothetical protein 5 | protein | 79 | 4% helix, 48% strand | P59636 |
| C, D, F, H | Hypothetical protein 5 | protein | 76 | 0% helix, 51% strand | P59636 |
| E, G | Hypothetical protein 5 | protein | 77 | 4% helix, 48% strand | P59636 |
Ligands and binding sites
- D10 · Decane · ligand · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.78 | 0.89 | 35 | D10 |
| 2 | 303 | 0.78 | 0.88 | 38 | D10 |
| 3 | 306 | 0.78 | 0.88 | 38 | D10 |
| 4 | 284 | 0.77 | 0.88 | 35 | D10 |
| 5 | 276 | 0.50 | 0.74 | 33 | empty |
Interfaces
7 interfaces between chains.
- G–H · 1618 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 1598 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 1583 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 1582 Ų buried · 45 hydrogen bonds · protein-protein
- B–E · 212 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2CME · The crystal structure of SARS coronavirus ORF-9b protein · the same entry in another collection · chain C against C, 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 P59636
- Elsewhere: RCSB PDB 2CME · PDBe 2CME · UniProt P59636
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