Research workbench
SIVMAC239 nef in complex with TCR zeta itam 1 polypeptide (A63-R80)
Analyse SIVMAC239 nef in complex with TCR zeta itam 1 polypeptide (A63-R80) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IK5
- Type
- protein
- Length
- 267 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein nef; T-cell surface glycoprotein CD3 zeta chain
- UniProt
- Q5QGG3, P20963
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein nef | protein | 119 | 33% helix, 13% strand | Q5QGG3 |
| C | Protein nef | protein | 117 | 33% helix, 14% strand | Q5QGG3 |
| D | T-cell surface glycoprotein CD3 zeta chain | protein | 15 | 67% helix, 0% strand | P20963 |
| B | T-cell surface glycoprotein CD3 zeta chain | protein | 16 | 75% helix, 0% strand | P20963 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.47 | 0.74 | 20 | empty |
| 2 | 77 | 0.33 | 0.75 | 22 | empty |
| 3 | 54 | 0.29 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 696 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 638 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 Q5QGG3
- Every structure of UniProt P20963
- Elsewhere: RCSB PDB 3IK5 · PDBe 3IK5 · UniProt Q5QGG3 · UniProt P20963
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