Research workbench
HIV-1 nef protein in complex with single domain antibody SDAB19 and an engineered hck SH3 domain
Analyse HIV-1 nef protein in complex with single domain antibody SDAB19 and an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ORZ
- Type
- protein
- Length
- 287 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase hck; Protein nef; Single domain antibody SDAB19
- EC
- 2.7.10.2
- UniProt
- P08631, P03407
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase hck (EC 2.7.10.2) | protein | 56 | 5% helix, 48% strand | P08631 |
| B | Protein nef | protein | 117 | 38% helix, 14% strand | P03407 |
| C | Single domain antibody SDAB19 | protein | 114 | 5% helix, 55% strand | — |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.47 | 0.85 | 15 | empty |
| 2 | 78 | 0.41 | 0.79 | 21 | empty |
| 3 | 75 | 0.35 | 0.76 | 19 | empty |
| 4 | 74 | 0.30 | 0.73 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–C · 780 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 649 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4ORZ · HIV-1 Nef protein in complex with single domain antibody sdAb19 and an engineered Hck SH3… · the same entry in another collection · chain A against A, TM-score 1.00
- P08631 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase hck (P08631) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P08631
- Every structure of UniProt P03407
- Elsewhere: RCSB PDB 4ORZ · PDBe 4ORZ · UniProt P08631 · UniProt P03407
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