Research workbench
Unliganded mature oxy-cope catalytic antibody
Analyse Unliganded mature oxy-cope catalytic antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D5B
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimeric oxy-cope catalytic antibody az-28 (light chain); Chimeric oxy-cope catalytic…
- UniProt
- Q7TS98, P01834, K7T9I5, P0DOX5
- Ligands
- CD
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Chimeric oxy-cope catalytic antibody az-28 (light chain) | protein | 211 | 6% helix, 51% strand | Q7TS98, P01834 |
| B, H | Chimeric oxy-cope catalytic antibody az-28 (heavy chain) | protein | 221 | 5% helix, 50% strand | K7T9I5, P0DOX5 |
Ligands and binding sites
- CD · Cadmium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.76 | 0.79 | 123 | empty |
| 2 | 262 | 0.56 | 0.77 | 32 | empty |
| 3 | 231 | 0.51 | 0.76 | 35 | empty |
| 4 | 132 | 0.44 | 0.76 | 17 | empty |
| 5 | 91 | 0.41 | 0.78 | 17 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1801 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1780 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 317 Ų buried · 9 hydrogen bonds · protein-protein
- B–H · 295 Ų buried · 3 hydrogen bonds · protein-protein
- A–L · 201 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 Q7TS98
- Every structure of UniProt P01834
- Every structure of UniProt K7T9I5
- Every structure of UniProt P0DOX5
- Elsewhere: RCSB PDB 1D5B · PDBe 1D5B · UniProt Q7TS98 · UniProt P01834 · UniProt K7T9I5 · UniProt P0DOX5
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