MolNFT v1 · #71155 · protein
Crystal structure of HCV NS3/4A protease in complex with N-terminal product 4B5A
3M5N: “Crystal structure of HCV NS3/4A protease in complex with N-terminal product 4B5A”. X-ray diffraction, 2 ligands (ZN, SO4), 4 pockets (best druggability 0.65). MolNFT v1 #71155 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3M5N
- Type
- protein
- Length
- 815 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3/4A; Secttpc peptide
- EC
- 3.4.21.98
- UniProt
- A8DG50, B3TKQ3
- Ligands
- ZN, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS3/4A (EC 3.4.21.98) | protein | 200 | 13% helix, 45% strand | A8DG50 |
| B | NS3/4A (EC 3.4.21.98) | protein | 199 | 14% helix, 43% strand | A8DG50 |
| C | NS3/4A (EC 3.4.21.98) | protein | 197 | 12% helix, 45% strand | A8DG50 |
| D | NS3/4A (EC 3.4.21.98) | protein | 198 | 12% helix, 43% strand | A8DG50 |
| F, G, H | Secttpc peptide | protein | 7 | 0% helix, 71% strand | B3TKQ3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.65 | 0.80 | 36 | empty |
| 2 | 189 | 0.47 | 0.76 | 29 | empty |
| 3 | 57 | 0.27 | 0.73 | 18 | empty |
| 4 | 55 | 0.26 | 0.72 | 16 | empty |
Interfaces
7 interfaces between chains.
- D–H · 445 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 435 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 431 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 143 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 94 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3M5N · Crystal structure of HCV NS3/4A protease in complex with N-terminal product 4B5A · 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 A8DG50
- Every structure of UniProt B3TKQ3
- Elsewhere: RCSB PDB 3M5N · PDBe 3M5N · UniProt A8DG50 · UniProt B3TKQ3
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