MolNFT v1 · #120108 · protein
Crystal structures of unlinked NS2B-NS3 protease from zika virus and its complex with a reverse peptide inhibitor
5GPI: “Crystal structures of unlinked NS2B-NS3 protease from zika virus and its complex with a reverse peptide…”. X-ray diffraction, 5 pockets (best druggability 0.65). MolNFT v1 #120108 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5GPI
- Type
- protein
- Length
- 760 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3 protease; NS2B cofactor
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 7 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | NS3 protease | protein | 153 | 5% helix, 47% strand | — |
| C | NS2B cofactor | protein | 37 | 0% helix, 46% strand | — |
| A, E | NS2B cofactor | protein | 38 | 0% helix, 47% strand | — |
| G | NS2B cofactor | protein | 40 | 0% helix, 45% strand | — |
| D | NS3 protease | protein | 148 | 3% helix, 47% strand | — |
| B | NS3 protease | protein | 154 | 5% helix, 47% strand | — |
| F | NS3 protease | protein | 152 | 5% helix, 47% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.65 | 0.76 | 63 | empty |
| 2 | 158 | 0.45 | 0.75 | 21 | empty |
| 3 | 141 | 0.44 | 0.76 | 24 | empty |
| 4 | 121 | 0.42 | 0.76 | 19 | empty |
| 5 | 119 | 0.41 | 0.75 | 22 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2036 Ų buried · 32 hydrogen bonds · protein-protein
- H–G · 1960 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1935 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 1914 Ų buried · 30 hydrogen bonds · protein-protein
- D–B · 387 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5GPI · Crystal Structures of Unlinked NS2B-NS3 Protease from Zika Virus and Its Complex with a… · the same entry in another collection · chain H against H, 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 5GPI · PDBe 5GPI
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