Research workbench
Crystal structure of HBV capsid Y132A mutant in complex with N-(3- chloro-4-fluorophenyl)-3-phenyl-1,4,6,7-tetrahydro-5H-PYRAZOLO[4,3- C]PYRIDINE-5-carboxamide at 2.65A resolution
Analyse Crystal structure of HBV capsid Y132A mutant in complex with N-(3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K5M
- Type
- protein
- Length
- 785 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- P03147
- Ligands
- VXJ
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 136 | 68% helix, 0% strand | P03147 |
| B | Capsid protein | protein | 132 | 67% helix, 0% strand | P03147 |
| C | Capsid protein | protein | 133 | 68% helix, 0% strand | P03147 |
| D | Capsid protein | protein | 131 | 67% helix, 0% strand | P03147 |
| E | Capsid protein | protein | 124 | 62% helix, 0% strand | P03147 |
| F | Capsid protein | protein | 129 | 66% helix, 0% strand | P03147 |
Ligands and binding sites
- VXJ · N-(3-chloro-4-fluorophenyl)-3-phenyl-2,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide · ligand · 6 copies · chains A, B, C, D, E, F
- IPA · Isopropyl alcohol · additive · 5 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.68 | 0.86 | 28 | VXJ |
| 2 | 201 | 0.68 | 0.85 | 27 | VXJ |
| 3 | 204 | 0.68 | 0.85 | 30 | VXJ |
| 4 | 199 | 0.66 | 0.84 | 25 | empty |
| 5 | 152 | 0.62 | 0.84 | 24 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1738 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1692 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1540 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 530 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 527 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7K5M · CRYSTAL STRUCTURE OF HBV CAPSID Y132A MUTANT IN COMPLEX WITH… · 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 P03147
- Elsewhere: RCSB PDB 7K5M · PDBe 7K5M · UniProt P03147
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