MolNFT v1 · #166581 · protein
Structure of anti-HCD33 conditional scfv
6UUP · Anti-CD33 conditional scfv: “Structure of anti-HCD33 conditional scfv”. X-ray diffraction, 1 ligand (K), 11 pockets (best druggability 0.67). MolNFT v1 #166581 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6UUP
- Type
- protein
- Length
- 911 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-CD33 conditional scfv
- Ligands
- K
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Anti-CD33 conditional scfv | protein | 227 | 3% helix, 49% strand | — |
| B | Anti-CD33 conditional scfv | protein | 228 | 3% helix, 49% strand | — |
| D | Anti-CD33 conditional scfv | protein | 229 | 3% helix, 48% strand | — |
Ligands and binding sites
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 19 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.67 | 0.86 | 40 | K, PEG |
| 2 | 152 | 0.61 | 0.85 | 37 | K, PEG |
| 3 | 243 | 0.54 | 0.77 | 39 | GOL |
| 4 | 120 | 0.49 | 0.79 | 23 | GOL |
| 5 | 119 | 0.48 | 0.79 | 24 | GOL |
Interfaces
5 interfaces between chains.
- C–D · 1187 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1056 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 342 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 222 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6UUP · Structure of anti-hCD33 conditional scFv · 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 6UUP · PDBe 6UUP
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