MolNFT v1 · #172504 · protein
Crystal structure of the aph coiled-coil in complex with nanobodies NB28 and NB30
7A4D · Nanobody NB28: “Crystal structure of the aph coiled-coil in complex with nanobodies NB28 and NB30”. X-ray diffraction, 2 ligands (ACE, NH2), 16 pockets (best druggability 0.73). MolNFT v1 #172504 on GenesisL1: 3D structure, binding…
- PDB
- 7A4D
- Type
- protein
- Length
- 1,082 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody NB28; Nanobody NB30; Aph coiled-coil
- Ligands
- ACE, NH2
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 7 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nanobody NB28 | protein | 118 | 8% helix, 42% strand | — |
| B | Nanobody NB28 | protein | 117 | 8% helix, 42% strand | — |
| C, I, J | Nanobody NB30 | protein | 113 | 3% helix, 45% strand | — |
| D | Nanobody NB30 | protein | 112 | 6% helix, 47% strand | — |
| E, F, K, L | Aph coiled-coil | protein | 40 | 95% helix, 0% strand | — |
| G | Nanobody NB28 | protein | 120 | 5% helix, 42% strand | — |
| H | Nanobody NB28 | protein | 116 | 5% helix, 42% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains D, E, F
- NH2 · Amino group · ion · chains E, G
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, H
- GOL · Glycerol · additive · chains D
- ACT · Acetate ion · additive · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.73 | 0.88 | 41 | ACT |
| 2 | 248 | 0.71 | 0.86 | 36 | empty |
| 3 | 292 | 0.63 | 0.80 | 33 | empty |
| 4 | 264 | 0.63 | 0.81 | 29 | empty |
| 5 | 355 | 0.56 | 0.75 | 48 | empty |
Interfaces
26 interfaces between chains.
- K–L · 1036 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1035 Ų buried · 6 hydrogen bonds · protein-protein
- G–K · 747 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 743 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 733 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 7A4D · Crystal structure of the APH coiled-coil in complex with nanobodies Nb28 and Nb30 · 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 7A4D · PDBe 7A4D
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