MolNFT v1 · #117180 · protein
Crystal structure of the HBV capsid Y132A mutant (vcid 8772) in complex with NVR10-001E2 at 1.95A resolution
5E0I · Capsid protein: “Crystal structure of the HBV capsid Y132A mutant (vcid 8772) in complex with NVR10-001E2 at 1.95A resolution”. X-ray diffraction, 1 ligand (5J6), 11 pockets (best druggability 0.71). MolNFT v1 #117180 on GenesisL1…
- PDB
- 5E0I
- Type
- protein
- Length
- 880 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- P03147
- Ligands
- 5J6
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Capsid protein | protein | 154 | 66% helix, 0% strand | P03147 |
| C | Capsid protein | protein | 146 | 65% helix, 0% strand | P03147 |
| D | Capsid protein | protein | 145 | 68% helix, 0% strand | P03147 |
| E | Capsid protein | protein | 144 | 65% helix, 0% strand | P03147 |
| F | Capsid protein | protein | 137 | 61% helix, 0% strand | P03147 |
Ligands and binding sites
- 5J6 · methyl 4-(2-bromo-4-fluorophenyl)-6-(morpholin-4-ylmethyl)-2-(1,3-thiazol-2-yl)pyrimidine-5-carboxylate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.71 | 0.80 | 49 | 5J6 |
| 2 | 508 | 0.71 | 0.80 | 44 | 5J6 |
| 3 | 535 | 0.71 | 0.80 | 43 | 5J6 |
| 4 | 118 | 0.61 | 0.86 | 29 | empty |
| 5 | 78 | 0.58 | 0.87 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2042 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1854 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1702 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 685 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 658 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5E0I · Crystal structure of the HBV capsid Y132A mutant (VCID 8772) in complex with NVR10-001E2… · 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 5E0I · PDBe 5E0I · UniProt P03147
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