Research workbench
Crystal structure of the anti-human P-cadherin Fab CQY684 in complex with human P-CADHERIN(108-324)
Analyse Crystal structure of the anti-human P-cadherin Fab CQY684 in complex with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZTR
- Type
- protein
- Length
- 1,305 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CQY684 Fab heavy-chain; CQY684 Fab light-chain; Cadherin-3
- UniProt
- P22223
- Ligands
- CA
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | CQY684 Fab heavy-chain | protein | 229 | 5% helix, 54% strand | — |
| B, L | CQY684 Fab light-chain | protein | 210 | 6% helix, 52% strand | — |
| I | Cadherin-3 | protein | 214 | 3% helix, 43% strand | P22223 |
| J | Cadherin-3 | protein | 213 | 3% helix, 44% strand | P22223 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.76 | 0.83 | 58 | empty |
| 2 | 918 | 0.76 | 0.79 | 80 | empty |
| 3 | 563 | 0.61 | 0.74 | 57 | empty |
| 4 | 66 | 0.54 | 0.88 | 21 | empty |
| 5 | 308 | 0.52 | 0.74 | 46 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1857 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1855 Ų buried · 14 hydrogen bonds · protein-protein
- B–J · 483 Ų buried · 5 hydrogen bonds · protein-protein
- I–L · 480 Ų buried · 3 hydrogen bonds · protein-protein
- H–I · 360 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6ZTR · Crystal Structure of the anti-human P-Cadherin Fab CQY684 in complex with human… · the same entry in another collection · chain L against L, TM-score 1.00
- P22223 · AlphaFold monomer V2.0 prediction for cadherin-3 (P22223) · a predicted model of the same protein · chain J against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P22223
- Elsewhere: RCSB PDB 6ZTR · PDBe 6ZTR · UniProt P22223
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