MolNFT v1 · #172521 · protein
Crystal structure of the aph coiled-coil in complex with nanobody NB26
7A50: “Crystal structure of the aph coiled-coil in complex with nanobody NB26”. X-ray diffraction, 2 ligands (ACE, NH2), 1 pocket (best druggability 0.43). MolNFT v1 #172521 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7A50
- Type
- protein
- Length
- 331 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody NB26; Coiled-coil aph
- Ligands
- ACE, NH2
- Pockets
- 1 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody NB26 | protein | 127 | 9% helix, 46% strand | — |
| B, D | Coiled-coil aph | protein | 40 | 95% helix, 0% strand | — |
| C | Nanobody NB26 | protein | 124 | 7% helix, 46% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, D
- NH2 · Amino group · ion · 2 copies · chains B, D
- EDO · 1,2-ethanediol · additive · 3 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.43 | 0.82 | 14 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1158 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 652 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 553 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 267 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 247 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 7A50 · Crystal structure of the APH coiled-coil in complex with nanobody Nb26 · 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 7A50 · PDBe 7A50
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