MolNFT v1 · #84332 · protein
The crystal structure of single domain antibody 2X1 scaffold
3ZHK · MG2X1 scaffold antibody: “The crystal structure of single domain antibody 2X1 scaffold”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.45). MolNFT v1 #84332 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3ZHK
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MG2X1 scaffold antibody
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MG2X1 scaffold antibody | protein | 119 | 5% helix, 52% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.45 | 0.74 | 32 | empty |
| 2 | 51 | 0.24 | 0.72 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 228 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3ZHK · The crystal structure of single domain antibody 2x1 scaffold · the same entry in another collection · chain B against B, 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 3ZHK · PDBe 3ZHK
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