Research workbench
Crystal structure of the single-chain fv fragment 1696 in complex with the epitope peptide corresponding to N- terminus of HIV-2 protease
Analyse Crystal structure of the single-chain fv fragment 1696 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SVZ
- Type
- protein
- Length
- 476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-chain fv fragment 1696; Epitope peptide corresponding to N-terminus of HIV-2…
- UniProt
- P01631
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Single-chain fv fragment 1696 | protein | 232 | 8% helix, 52% strand | P01631 |
| C, D | Epitope peptide corresponding to N-terminus of HIV-2 protease | protein | 6 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.81 | 0.83 | 104 | empty |
| 2 | 205 | 0.58 | 0.80 | 34 | empty |
| 3 | 50 | 0.28 | 0.75 | 15 | empty |
| 4 | 57 | 0.26 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 840 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 584 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 581 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1SVZ · Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope… · the same entry in another collection · chain A against A, TM-score 1.00
- P01631 · AlphaFold monomer V2.0 prediction for ig kappa chain V-II region 26-10 (P01631) · a predicted model of the same protein · chain A against A, TM-score 0.48
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 P01631
- Elsewhere: RCSB PDB 1SVZ · PDBe 1SVZ · UniProt P01631
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