Research workbench
Crystal structure of the P5P6 coiled-coil in complex with nanobody NB34.
Analyse Crystal structure of the P5P6 coiled-coil in complex with nanobody NB34. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A4Y
- Type
- protein
- Length
- 399 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody NB34; Coiled-coil P6 peptide; Coiled-coil P5 peptide
- Ligands
- ACE, SO4, NH2
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nanobody NB34 | protein | 113 | 10% helix, 46% strand | — |
| B | Nanobody NB34 | protein | 115 | 10% helix, 46% strand | — |
| D | Coiled-coil P6 peptide | protein | 29 | 93% helix, 0% strand | — |
| E | Coiled-coil P5 peptide | protein | 29 | 86% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains D, E
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, E, C, D
- NH2 · Amino group · ion · 2 copies · chains D, E
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.61 | 0.76 | 66 | SO4 |
Interfaces
6 interfaces between chains.
- D–E · 807 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 532 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 397 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 320 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 299 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 7A4Y · Crystal structure of the P5P6 coiled-coil in complex with nanobody Nb34. · 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
- Elsewhere: RCSB PDB 7A4Y · PDBe 7A4Y
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