MolNFT v1 · #120030 · protein
Hepatitis B virus core protein Y132A mutant in complex with 4-methyl heteroaryldihydropyrimidine
5GMZ: “Hepatitis B virus core protein Y132A mutant in complex with 4-methyl heteroaryldihydropyrimidine”. X-ray diffraction, 2 ligands (6XU, CL), 10 pockets (best druggability 0.72). MolNFT v1 #120030 on GenesisL1: 3D structure, binding…
- PDB
- 5GMZ
- Type
- protein
- Length
- 877 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core protein
- UniProt
- L7R9I1
- Ligands
- 6XU, CL
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Core protein | protein | 143 | 71% helix, 0% strand | L7R9I1 |
| B | Core protein | protein | 148 | 69% helix, 0% strand | L7R9I1 |
| D | Core protein | protein | 150 | 69% helix, 0% strand | L7R9I1 |
| F | Core protein | protein | 150 | 66% helix, 0% strand | L7R9I1 |
Ligands and binding sites
- 6XU · (2S)-4,4-difluoro-1-[[(4S)-4-(4-fluorophenyl)-5-methoxycarbonyl-4-methyl-2-(1,3-thiazol-2-yl)-1H-pyrimidin-6-yl]methyl]pyrrolidine-2-carboxylic acid · ligand · 7 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · chains D
- IPA · Isopropyl alcohol · additive · 11 copies · chains A, B, F, C, D, E
- GOL · Glycerol · additive · 2 copies · chains B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.72 | 0.86 | 31 | 6XU |
| 2 | 299 | 0.69 | 0.83 | 31 | 6XU |
| 3 | 293 | 0.69 | 0.83 | 31 | 6XU |
| 4 | 64 | 0.40 | 0.80 | 14 | empty |
| 5 | 61 | 0.32 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2059 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1990 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1928 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 511 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 498 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5GMZ · Hepatitis B virus core protein Y132A mutant in complex with 4-methyl… · 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 L7R9I1
- Elsewhere: RCSB PDB 5GMZ · PDBe 5GMZ · UniProt L7R9I1
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