Research workbench
Hepatitis B core-antigen in complex with scfv E13
Analyse Hepatitis B core-antigen in complex with scfv E13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CWD
- Type
- protein
- Length
- 1,442 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single chain variable fragment (scfv) E13; Capsid protein
- UniProt
- P03147
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, G, A | Single chain variable fragment (scfv) E13 | protein | 231 | 4% helix, 49% strand | — |
| D | Capsid protein | protein | 133 | 58% helix, 0% strand | P03147 |
| H | Capsid protein | protein | 131 | 60% helix, 0% strand | P03147 |
| C | Capsid protein | protein | 129 | 58% helix, 0% strand | P03147 |
| E | Single chain variable fragment (scfv) E13 | protein | 229 | 3% helix, 48% strand | — |
| F | Capsid protein | protein | 127 | 60% helix, 0% strand | P03147 |
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.73 | 0.80 | 74 | empty |
| 2 | 619 | 0.73 | 0.80 | 61 | empty |
| 3 | 900 | 0.73 | 0.77 | 82 | empty |
| 4 | 283 | 0.62 | 0.80 | 31 | empty |
| 5 | 254 | 0.54 | 0.76 | 32 | empty |
Interfaces
9 interfaces between chains.
- A–C · 1119 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1083 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1057 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1055 Ų buried · 21 hydrogen bonds · protein-protein
- D–H · 797 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6CWD · Hepatitis B core-antigen in complex with scFv e13 · 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 6CWD · PDBe 6CWD · UniProt P03147
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