Research workbench
Structure of anti-HCD33 conditional scfv with methotrexate
Analyse Structure of anti-HCD33 conditional scfv with methotrexate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UY3
- Type
- protein
- Length
- 236 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-CD33 conditional scfv
- Ligands
- MTX, PO4
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-CD33 conditional scfv | protein | 236 | 4% helix, 49% strand | — |
Ligands and binding sites
- MTX · Methotrexate · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.60 | 0.86 | 21 | MTX |
| 2 | 134 | 0.46 | 0.77 | 24 | GOL |
| 3 | 87 | 0.33 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6UY3 · Structure of anti-hCD33 conditional scFv with methotrexate · 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 6UY3 · PDBe 6UY3
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