Research workbench
Crystal structure of the gcn coiled-coil in complex with nanobody NB39
Analyse Crystal structure of the gcn coiled-coil in complex with nanobody NB39 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A4T
- Type
- protein
- Length
- 175 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody NB39; GCN4 isoform 1
- UniProt
- A0A6A5PZY2
- Ligands
- ACE, SO4
- Pockets
- 1 · best druggability 0.36
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody NB39 | protein | 121 | 5% helix, 58% strand | — |
| B | GCN4 isoform 1 | protein | 26 | 92% helix, 0% strand | A0A6A5PZY2 |
| C | GCN4 isoform 1 | protein | 28 | 89% helix, 0% strand | A0A6A5PZY2 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.36 | 0.77 | 13 | SO4 |
Interfaces
3 interfaces between chains.
- A–C · 780 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 731 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 184 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 7A4T · Crystal structure of the GCN coiled-coil in complex with nanobody Nb39 · 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 A0A6A5PZY2
- Elsewhere: RCSB PDB 7A4T · PDBe 7A4T · UniProt A0A6A5PZY2
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